data_25116 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR data-driven model of GTPase KRas-GNP:ARafRBD complex tethered to a lipid-bilayer nanodisc ; _BMRB_accession_number 25116 _BMRB_flat_file_name bmr25116.str _Entry_type original _Submission_date 2014-07-29 _Accession_date 2014-07-29 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; This is a hybrid model generated by Haddock docking simulation that is based on i) NMR data that includes PRE-measurements between lipids (i.e. nanodisc) and the protien (i.e. K-RasGNP and A-RafRBD) ii) crystolagraphic information (K-RasGNP and A-RafRBD) and iii) theoretical computation (i.e. nanodisc). ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mazhab-Jafari 'Mohammad T.' . . 2 Stathopoulos 'Peter B.' . . 3 Marshall 'Christopher B.' . . 4 Ikura Mitsuhiko . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 13 "13C chemical shifts" 13 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-10-12 update BMRB 'update entry citation' 2015-05-27 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 25114 'GTPase KRas-GDP tethered to a lipid-bilayer nanodisc' 25115 'GTPase KRas-GNP tethered to a lipid-bilayer nanodisc' stop_ _Original_release_date 2015-05-27 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25941399 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mazhab-Jafari 'Mohammad T.' . . 2 Marshall 'Christopher B.' . . 3 Smith 'Matthew J.' . . 4 Gasmi-Seabrook 'Genevieve M. C.' . . 5 Stathopoulos 'Peter B.' . . 6 Inagaki Fuyuhiko . . 7 Kay 'Lewis E.' . . 8 Neel 'Benjamin G.' . . 9 Ikura Mitsuhiko . . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U. S. A.' _Journal_volume 112 _Journal_issue 21 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6625 _Page_last 6630 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'GTPase KRas-GNP:ARafRBD complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label K-Ras $K-Ras 'membrane scaffold protein' $membrane_scaffold_protein A-RafRBD $A-RafRBD stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_K-Ras _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common K-Ras _Molecular_mass 8696.952 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 187 _Mol_residue_sequence ; GSMTEYKLVVVGAGGVGKSA LTIQLIQNHFVDEYDPTIED SYRKQVVIDGETCLLDILDT AGQEEYSAMRDQYMRTGEGF LCVFAINNTKSFEDIHHYRE QIKRVKDSEDVPMVLVGNKC DLPSRTVDTKQAQDLARSYG IPFIETSAKTRQGVDDAFYT LVREIRKHKEKMSKDGKKKK KKSKTKC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -1 GLY 2 0 SER 3 1 MET 4 2 THR 5 3 GLU 6 4 TYR 7 5 LYS 8 6 LEU 9 7 VAL 10 8 VAL 11 9 VAL 12 10 GLY 13 11 ALA 14 12 GLY 15 13 GLY 16 14 VAL 17 15 GLY 18 16 LYS 19 17 SER 20 18 ALA 21 19 LEU 22 20 THR 23 21 ILE 24 22 GLN 25 23 LEU 26 24 ILE 27 25 GLN 28 26 ASN 29 27 HIS 30 28 PHE 31 29 VAL 32 30 ASP 33 31 GLU 34 32 TYR 35 33 ASP 36 34 PRO 37 35 THR 38 36 ILE 39 37 GLU 40 38 ASP 41 39 SER 42 40 TYR 43 41 ARG 44 42 LYS 45 43 GLN 46 44 VAL 47 45 VAL 48 46 ILE 49 47 ASP 50 48 GLY 51 49 GLU 52 50 THR 53 51 CYS 54 52 LEU 55 53 LEU 56 54 ASP 57 55 ILE 58 56 LEU 59 57 ASP 60 58 THR 61 59 ALA 62 60 GLY 63 61 GLN 64 62 GLU 65 63 GLU 66 64 TYR 67 65 SER 68 66 ALA 69 67 MET 70 68 ARG 71 69 ASP 72 70 GLN 73 71 TYR 74 72 MET 75 73 ARG 76 74 THR 77 75 GLY 78 76 GLU 79 77 GLY 80 78 PHE 81 79 LEU 82 80 CYS 83 81 VAL 84 82 PHE 85 83 ALA 86 84 ILE 87 85 ASN 88 86 ASN 89 87 THR 90 88 LYS 91 89 SER 92 90 PHE 93 91 GLU 94 92 ASP 95 93 ILE 96 94 HIS 97 95 HIS 98 96 TYR 99 97 ARG 100 98 GLU 101 99 GLN 102 100 ILE 103 101 LYS 104 102 ARG 105 103 VAL 106 104 LYS 107 105 ASP 108 106 SER 109 107 GLU 110 108 ASP 111 109 VAL 112 110 PRO 113 111 MET 114 112 VAL 115 113 LEU 116 114 VAL 117 115 GLY 118 116 ASN 119 117 LYS 120 118 CYS 121 119 ASP 122 120 LEU 123 121 PRO 124 122 SER 125 123 ARG 126 124 THR 127 125 VAL 128 126 ASP 129 127 THR 130 128 LYS 131 129 GLN 132 130 ALA 133 131 GLN 134 132 ASP 135 133 LEU 136 134 ALA 137 135 ARG 138 136 SER 139 137 TYR 140 138 GLY 141 139 ILE 142 140 PRO 143 141 PHE 144 142 ILE 145 143 GLU 146 144 THR 147 145 SER 148 146 ALA 149 147 LYS 150 148 THR 151 149 ARG 152 150 GLN 153 151 GLY 154 152 VAL 155 153 ASP 156 154 ASP 157 155 ALA 158 156 PHE 159 157 TYR 160 158 THR 161 159 LEU 162 160 VAL 163 161 ARG 164 162 GLU 165 163 ILE 166 164 ARG 167 165 LYS 168 166 HIS 169 167 LYS 170 168 GLU 171 169 LYS 172 170 MET 173 171 SER 174 172 LYS 175 173 ASP 176 174 GLY 177 175 LYS 178 176 LYS 179 177 LYS 180 178 LYS 181 179 LYS 182 180 LYS 183 181 SER 184 182 LYS 185 183 THR 186 184 LYS 187 185 CYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-25 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 17785 KRas171 91.44 171 100.00 100.00 1.71e-122 BMRB 18529 K-Ras 88.77 169 100.00 100.00 1.20e-118 BMRB 25114 K-Ras 100.00 187 100.00 100.00 4.15e-134 BMRB 25115 K-Ras 100.00 187 100.00 100.00 4.15e-134 BMRB 26635 K-Ras4B 98.93 188 100.00 100.00 9.48e-133 PDB 2MSC "Nmr Data-driven Model Of Gtpase Kras-gdp Tethered To A Lipid-bilayer Nanodisc" 100.00 187 100.00 100.00 4.15e-134 PDB 2MSD "Nmr Data-driven Model Of Gtpase Kras-gnp Tethered To A Lipid-bilayer Nanodisc" 100.00 187 100.00 100.00 4.15e-134 PDB 2MSE "Nmr Data-driven Model Of Gtpase Kras-gnp:arafrbd Complex Tethered To A Lipid-bilayer Nanodisc" 100.00 187 100.00 100.00 4.15e-134 PDB 3GFT "Human K-ras (q61h) In Complex With A Gtp Analogue" 90.37 187 99.41 99.41 6.58e-120 PDB 4DSN "Small-Molecule Ligands Bind To A Distinct Pocket In Ras And Inhibit Sos-Mediated Nucleotide Exchange Activity" 98.40 189 99.46 99.46 1.71e-130 PDB 4DSO "Small-Molecule Ligands Bind To A Distinct Pocket In Ras And Inhibit Sos-Mediated Nucleotide Exchange Activity" 98.40 189 99.46 99.46 1.71e-130 PDB 4DST "Small-Molecule Ligands Bind To A Distinct Pocket In Ras And Inhibit Sos-Mediated Nucleotide Exchange Activity" 98.40 189 99.46 99.46 1.71e-130 PDB 4DSU "Small-Molecule Ligands Bind To A Distinct Pocket In Ras And Inhibit Sos-Mediated Nucleotide Exchange Activity" 98.40 189 99.46 99.46 1.71e-130 PDB 4EPR "Discovery Of Small Molecules That Bind To K-Ras And Inhibit Sos- Mediated Activation" 90.37 170 98.82 98.82 2.15e-118 PDB 4EPT "Discovery Of Small Molecules That Bind To K-Ras And Inhibit Sos- Mediated Activation" 90.37 170 99.41 99.41 1.28e-119 PDB 4EPV "Discovery Of Small Molecules That Bind To K-Ras And Inhibit Sos- Mediated Activation" 90.37 170 99.41 99.41 1.28e-119 PDB 4EPW "Discovery Of Small Molecules That Bind To K-Ras And Inhibit Sos- Mediated Activation" 90.37 170 99.41 99.41 1.28e-119 PDB 4EPX "Discovery Of Small Molecules That Bind To K-Ras And Inhibit Sos- Mediated Activation" 90.37 170 98.82 98.82 2.08e-118 PDB 4EPY "Discovery Of Small Molecules That Bind To K-Ras And Inhibit Sos- Mediated Activation" 90.37 170 98.82 98.82 2.08e-118 PDB 4L8G "Crystal Structure Of K-ras G12c, Gdp-bound" 90.37 170 99.41 99.41 3.29e-119 PDB 4LDJ "Crystal Structure Of A Gdp-bound G12c Oncogenic Mutant Of Human Gtpase Kras" 90.37 170 99.41 99.41 3.29e-119 PDB 4LPK "Crystal Structure Of K-ras Wt, Gdp-bound" 90.37 170 100.00 100.00 6.94e-121 PDB 4LRW "Crystal Structure Of K-ras G12c (cysteine-light), Gdp-bound" 90.37 170 97.63 97.63 5.67e-116 PDB 4LUC "Crystal Structure Of Small Molecule Disulfide 6 Bound To K-ras G12c" 90.37 170 97.63 97.63 5.67e-116 PDB 4LV6 "Crystal Structure Of Small Molecule Disulfide 4 Covalently Bound To K- Ras G12c" 90.37 170 97.63 97.63 5.67e-116 PDB 4LYF "Crystal Structure Of Small Molecule Vinylsulfonamide 8 Covalently Bound To K-ras G12c" 90.37 170 97.63 97.63 5.67e-116 PDB 4LYH "Crystal Structure Of Small Molecule Vinylsulfonamide 9 Covalently Bound To K-ras G12c" 90.37 170 97.63 97.63 5.67e-116 PDB 4LYJ "Crystal Structure Of Small Molecule Vinylsulfonamide 9 Covalently Bound To K-ras G12c, Alternative Space Group" 90.37 170 97.63 97.63 5.67e-116 PDB 4M1O "Crystal Structure Of Small Molecule Vinylsulfonamide 7 Covalently Bound To K-ras G12c" 90.37 170 97.63 97.63 5.67e-116 PDB 4M1S "Crystal Structure Of Small Molecule Vinylsulfonamide 13 Covalently Bound To K-ras G12c" 90.37 170 97.63 97.63 5.67e-116 PDB 4M1T "Crystal Structure Of Small Molecule Vinylsulfonamide 14 Covalently Bound To K-ras G12c" 90.37 170 97.63 97.63 5.67e-116 PDB 4M1W "Crystal Structure Of Small Molecule Vinylsulfonamide Covalently Bound To K-ras G12c" 90.37 170 97.63 97.63 5.67e-116 PDB 4M1Y "Crystal Structure Of Small Molecule Vinylsulfonamide 15 Covalently Bound To K-ras G12c" 90.37 170 97.63 97.63 5.67e-116 PDB 4M21 "Crystal Structure Of Small Molecule Acrylamide 11 Covalently Bound To K-ras G12c" 90.37 170 97.63 97.63 5.67e-116 PDB 4M22 "Crystal Structure Of Small Molecule Acrylamide 16 Covalently Bound To K-ras G12c" 90.37 170 97.63 97.63 5.67e-116 PDB 4NMM "Crystal Structure Of A G12c Oncogenic Variant Of Human Kras Bound To A Novel Gdp Competitive Covalent Inhibitor" 90.37 170 99.41 99.41 3.29e-119 PDB 4OBE "Crystal Structure Of Gdp-bound Human Kras" 90.37 170 100.00 100.00 6.94e-121 PDB 4PZY "Second-site Screening Of K-ras In The Presence Of Covalently Attached First-site Ligands" 90.37 170 98.22 98.22 1.18e-116 PDB 4PZZ "Second-site Screening Of K-ras In The Presence Of Covalently Attached First-site Ligands" 90.37 170 98.22 98.22 3.94e-117 PDB 4Q01 "Second-site Screening Of K-ras In The Presence Of Covalently Attached First-site Ligands" 90.37 169 98.22 98.22 3.89e-117 PDB 4Q02 "Second-site Screening Of K-ras In The Presence Of Covalently Attached First-site Ligands" 90.37 170 98.22 98.22 3.94e-117 PDB 4Q03 "Second-site Screening Of K-ras In The Presence Of Covalently Attached First-site Ligands" 90.37 170 98.22 98.22 3.94e-117 PDB 4QL3 "Crystal Structure Of A Gdp-bound G12r Oncogenic Mutant Of Human Gtpase Kras" 90.37 170 99.41 99.41 1.42e-119 PDB 4TQ9 "Crystal Structure Of A Gdp-bound G12v Oncogenic Mutant Of Human Gtpase Kras" 89.84 169 99.40 99.40 8.13e-119 PDB 4TQA "Crystal Structure Of A Gdp-bound G13d Oncogenic Mutant Of Human Gtpase Kras" 89.84 169 99.40 99.40 4.56e-119 PDB 4WA7 "Crystal Structure Of A Gdp-bound Q61l Oncogenic Mutant Of Human Gt- Pase Kras" 90.37 170 99.41 99.41 1.33e-119 DBJ BAE33023 "unnamed protein product [Mus musculus]" 98.93 188 97.84 99.46 1.67e-130 DBJ BAE37609 "unnamed protein product [Mus musculus]" 98.93 188 98.38 100.00 2.09e-131 DBJ BAF85199 "unnamed protein product [Homo sapiens]" 98.93 188 100.00 100.00 9.48e-133 DBJ BAJ17756 "v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog [synthetic construct]" 98.93 188 100.00 100.00 9.48e-133 EMBL CAA25624 "p21 protein [Homo sapiens]" 59.89 112 97.32 98.21 9.35e-73 EMBL CAA26295 "k-ras cellular oncogene [Mus musculus]" 98.93 188 98.38 100.00 2.09e-131 EMBL CAA37336 "K-ras [Xenopus laevis]" 98.93 187 97.84 97.84 3.33e-127 EMBL CAA59755 "turkey K-Ras [Meleagris gallopavo]" 98.93 188 99.46 100.00 2.92e-132 EMBL CAA76678 "p21-ras protein [Platichthys flesus]" 98.93 188 99.46 100.00 2.51e-132 GB AAA35689 "PR310 c-K-ras oncogene, partial [Homo sapiens]" 80.21 150 98.00 98.67 1.17e-103 GB AAA35690 "PR371 c-K-ras oncogene, partial [Homo sapiens]" 80.21 150 98.00 98.67 3.85e-103 GB AAA36554 "c-Ki-ras p21 protein, partial [Homo sapiens]" 51.34 96 98.96 98.96 1.52e-62 GB AAA42011 "Ki-ras protein, partial [Rattus norvegicus]" 51.34 96 97.92 97.92 5.54e-61 GB AAA49429 "ras-1 protein, partial [Oncorhynchus mykiss]" 73.26 137 97.81 99.27 6.93e-94 PIR A54321 "transforming protein c-Ki-ras-1, hepatic - rainbow trout (fragment)" 91.98 172 99.42 100.00 9.28e-123 PRF 0909262B "protein c-Ki-ras2" 98.93 188 100.00 100.00 9.48e-133 REF NP_001003744 "GTPase KRas [Danio rerio]" 98.93 188 97.30 98.38 8.75e-129 REF NP_001028153 "GTPase KRas precursor [Monodelphis domestica]" 98.93 188 99.46 99.46 2.24e-131 REF NP_001095209 "GTPase KRas precursor [Xenopus laevis]" 98.93 187 97.84 97.84 3.33e-127 REF NP_001103471 "GTPase KRas [Bos taurus]" 98.93 188 100.00 100.00 1.07e-132 REF NP_001184192 "uncharacterized protein LOC100505423 [Xenopus laevis]" 98.93 187 98.92 98.92 2.59e-129 SP O42277 "RecName: Full=GTPase KRas; AltName: Full=Ki-Ras; Short=K-ras; Flags: Precursor" 98.93 188 98.38 100.00 3.14e-131 SP P79800 "RecName: Full=GTPase KRas; AltName: Full=K-Ras 2; AltName: Full=Ki-Ras; Short=K-ras; Flags: Precursor" 98.93 188 99.46 100.00 2.92e-132 SP Q05147 "RecName: Full=GTPase KRas; AltName: Full=Ki-Ras; Short=K-ras; Flags: Precursor" 98.93 187 97.84 97.84 3.33e-127 SP Q07983 "RecName: Full=GTPase KRas; AltName: Full=K-Ras 2; AltName: Full=Ki-Ras; AltName: Full=c-K-ras; AltName: Full=c-Ki-ras; Contains" 98.93 188 99.46 99.46 2.24e-131 SP Q5EFX7 "RecName: Full=GTPase KRas; AltName: Full=Ki-Ras; Short=K-ras; Flags: Precursor" 98.93 188 98.38 99.46 5.04e-130 TPG DAA29418 "TPA: v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog [Bos taurus]" 98.93 188 100.00 100.00 1.07e-132 stop_ save_ save_membrane_scaffold_protein _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common membrane_scaffold_protein _Molecular_mass 63628.461 _Mol_thiol_state 'not present' _Details . _Residue_count 200 _Mol_residue_sequence ; GPLKLLDNWDSVTSTFSKLR EQLGPVTQEFWDNLEKETEG LRQEMSKDLEEVKAKVQPYL DDFQKKWQEEMELYRQKVEP LRAELQEGARQKLHELQEKL SPLGEEMRDRARAHVDALRT HLAPYSDELRQRLAARLEAL KENGGARLAEYHAKATEHLS TLSEKAKPALEDLRGELLPV LESFKVSFLSALEEYTKKLN ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 PRO 3 LEU 4 LYS 5 LEU 6 LEU 7 ASP 8 ASN 9 TRP 10 ASP 11 SER 12 VAL 13 THR 14 SER 15 THR 16 PHE 17 SER 18 LYS 19 LEU 20 ARG 21 GLU 22 GLN 23 LEU 24 GLY 25 PRO 26 VAL 27 THR 28 GLN 29 GLU 30 PHE 31 TRP 32 ASP 33 ASN 34 LEU 35 GLU 36 LYS 37 GLU 38 THR 39 GLU 40 GLY 41 LEU 42 ARG 43 GLN 44 GLU 45 MET 46 SER 47 LYS 48 ASP 49 LEU 50 GLU 51 GLU 52 VAL 53 LYS 54 ALA 55 LYS 56 VAL 57 GLN 58 PRO 59 TYR 60 LEU 61 ASP 62 ASP 63 PHE 64 GLN 65 LYS 66 LYS 67 TRP 68 GLN 69 GLU 70 GLU 71 MET 72 GLU 73 LEU 74 TYR 75 ARG 76 GLN 77 LYS 78 VAL 79 GLU 80 PRO 81 LEU 82 ARG 83 ALA 84 GLU 85 LEU 86 GLN 87 GLU 88 GLY 89 ALA 90 ARG 91 GLN 92 LYS 93 LEU 94 HIS 95 GLU 96 LEU 97 GLN 98 GLU 99 LYS 100 LEU 101 SER 102 PRO 103 LEU 104 GLY 105 GLU 106 GLU 107 MET 108 ARG 109 ASP 110 ARG 111 ALA 112 ARG 113 ALA 114 HIS 115 VAL 116 ASP 117 ALA 118 LEU 119 ARG 120 THR 121 HIS 122 LEU 123 ALA 124 PRO 125 TYR 126 SER 127 ASP 128 GLU 129 LEU 130 ARG 131 GLN 132 ARG 133 LEU 134 ALA 135 ALA 136 ARG 137 LEU 138 GLU 139 ALA 140 LEU 141 LYS 142 GLU 143 ASN 144 GLY 145 GLY 146 ALA 147 ARG 148 LEU 149 ALA 150 GLU 151 TYR 152 HIS 153 ALA 154 LYS 155 ALA 156 THR 157 GLU 158 HIS 159 LEU 160 SER 161 THR 162 LEU 163 SER 164 GLU 165 LYS 166 ALA 167 LYS 168 PRO 169 ALA 170 LEU 171 GLU 172 ASP 173 LEU 174 ARG 175 GLY 176 GLU 177 LEU 178 LEU 179 PRO 180 VAL 181 LEU 182 GLU 183 SER 184 PHE 185 LYS 186 VAL 187 SER 188 PHE 189 LEU 190 SER 191 ALA 192 LEU 193 GLU 194 GLU 195 TYR 196 THR 197 LYS 198 LYS 199 LEU 200 ASN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_A-RafRBD _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common A-RafRBD _Molecular_mass . _Mol_thiol_state . _Details . _Residue_count 73 _Mol_residue_sequence ; GTVKVYLPNKQRTVVTVRDG MSVYDSLDKALKVRGLNQDC CVVYRLIKGRKTVTAWDTAI APLDGEELIVEVL ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 808 GLY 2 809 THR 3 810 VAL 4 811 LYS 5 812 VAL 6 813 TYR 7 814 LEU 8 815 PRO 9 816 ASN 10 817 LYS 11 818 GLN 12 819 ARG 13 820 THR 14 821 VAL 15 822 VAL 16 823 THR 17 824 VAL 18 825 ARG 19 826 ASP 20 827 GLY 21 828 MET 22 829 SER 23 830 VAL 24 831 TYR 25 832 ASP 26 833 SER 27 834 LEU 28 835 ASP 29 836 LYS 30 837 ALA 31 838 LEU 32 839 LYS 33 840 VAL 34 841 ARG 35 842 GLY 36 843 LEU 37 844 ASN 38 845 GLN 39 846 ASP 40 847 CYS 41 848 CYS 42 849 VAL 43 850 VAL 44 851 TYR 45 852 ARG 46 853 LEU 47 854 ILE 48 855 LYS 49 856 GLY 50 857 ARG 51 858 LYS 52 859 THR 53 860 VAL 54 861 THR 55 862 ALA 56 863 TRP 57 864 ASP 58 865 THR 59 866 ALA 60 867 ILE 61 868 ALA 62 869 PRO 63 870 LEU 64 871 ASP 65 872 GLY 66 873 GLU 67 874 GLU 68 875 LEU 69 876 ILE 70 877 VAL 71 878 GLU 72 879 VAL 73 880 LEU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $K-Ras 'E. coli' 562 Bacteria . Escherichia coli $membrane_scaffold_protein 'E. coli' 562 Bacteria . Escherichia coli stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $K-Ras 'recombinant technology' . Escherichia coli . pET-28 $membrane_scaffold_protein 'recombinant technology' . Escherichia coli . 'pGBHPS MSP' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $K-Ras 0.6 mM 'U-15N, Ile C-delta-13C' $membrane_scaffold_protein 0.6 mM 'natural abundance' $A-RafRBD 0.7 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' Magnesium 5 mM 'natural abundance' TRIS 20 mM 'natural abundance' TCEP 2 mM 'natural abundance' 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 0.6 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phosphocholine 18.75 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phospho-L-serine 5 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide] 1.25 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $K-Ras 0.7 mM 'natural abundance' $membrane_scaffold_protein 0.7 mM 'natural abundance' $A-RafRBD 0.6 mM 'U-15N, Ile C-delta-13C' Magnesium 5 mM 'natural abundance' TRIS 20 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' TCEP 2 mM 'natural abundance' 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 0.7 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phosphocholine 18.75 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phospho-L-serine 5 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide] 1.25 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $K-Ras 0.6 mM 'U-15N, Ile C-delta-13C' $A-RafRBD 0.7 mM 'natural abundance' $membrane_scaffold_protein 0.6 mM 'natural abundance' TRIS 20 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' Magnesium 5 mM 'natural abundance' TCEP 2 mM 'natural abundance' 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 0.6 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phosphocholine 18.75 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phospho-L-serine 5 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide] 1.25 mM 'natural abundance' '1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)' 0.65 mM 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $K-Ras 0.7 mM 'natural abundance' $A-RafRBD 0.6 mM 'U-15N, Ile C-delta-13C' $membrane_scaffold_protein 0.7 mM 'natural abundance' TRIS 20 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' Magnesium 5 mM 'natural abundance' TCEP 2 mM 'natural abundance' 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' 0.7 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phosphocholine 18.75 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phospho-L-serine 5 mM 'natural abundance' 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide] 1.25 mM 'natural abundance' '1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)' 0.65 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details 'CNS was used in all structure calculation using Haddock scripts' save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRDraw _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_CHARMM-GUI _Saveframe_category software _Name CHARMM-GUI _Version . loop_ _Vendor _Address _Electronic_address 'CHARMM-GUI (S. Jo, T. Kim, V.G. Iyer, and W. Im)' . http://www.charmm-gui.org/ stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_HADDOCK _Saveframe_category software _Name HADDOCK _Version . loop_ _Vendor _Address _Electronic_address 'Alexandre Bonvin' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HMQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HMQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMQC' _Sample_label $sample_2 save_ save_2D_1H-13C_HMQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMQC' _Sample_label $sample_3 save_ save_2D_1H-13C_HMQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMQC' _Sample_label $sample_4 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.105 . M pH 7.4 . pH pressure 1 . atm temperature 298.2 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio water C 13 protons ppm 4.7 internal indirect . . . 0.25144920 water H 1 protons ppm 4.7 internal direct . . . 1 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details ; K-RAS isoleucine C -methyl resonances were first tentatively assigned based on assignments of T35S H-RAS-GMPPNP (BMRB code: 17610), and then remaining ambiguous assignments were resolved by mutagenesis of isoleucines 21, 36, 100, 139, and 163 to leucine residues. The A-RAFRBD isoleucine C -methyl resonance assignments were transferred from BMRB entry: 11265. ; loop_ _Experiment_label '2D 1H-13C HMQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name K-Ras _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 21 23 ILE HD1 H 0.565 . 1 2 21 23 ILE CD1 C 10.043 . 1 3 24 26 ILE HD1 H 0.379 . 1 4 24 26 ILE CD1 C 8.757 . 1 5 36 38 ILE HD1 H 0.550 . 1 6 36 38 ILE CD1 C 11.108 . 1 7 46 48 ILE HD1 H 0.381 . 1 8 46 48 ILE CD1 C 12.585 . 1 9 55 57 ILE HD1 H 0.472 . 1 10 55 57 ILE CD1 C 12.518 . 1 11 84 86 ILE HD1 H 0.705 . 1 12 84 86 ILE CD1 C 12.648 . 1 13 93 95 ILE HD1 H 0.728 . 1 14 93 95 ILE CD1 C 6.618 . 1 15 100 102 ILE HD1 H 0.245 . 1 16 100 102 ILE CD1 C 12.710 . 1 17 139 141 ILE HD1 H 0.835 . 1 18 139 141 ILE CD1 C 12.698 . 1 19 142 144 ILE HD1 H 0.619 . 1 20 142 144 ILE CD1 C 11.108 . 1 stop_ save_ save_assigned_chem_shift_list_1_3 _Saveframe_category assigned_chemical_shifts _Details ; K-RAS isoleucine C -methyl resonances were first tentatively assigned based on assignments of T35S H-RAS-GMPPNP (BMRB code: 17610), and then remaining ambiguous assignments were resolved by mutagenesis of isoleucines 21, 36, 100, 139, and 163 to leucine residues. The A-RAFRBD isoleucine C -methyl resonance assignments were transferred from BMRB entry: 11265. ; loop_ _Experiment_label '2D 1H-13C HMQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name A-RafRBD _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 854 47 ILE HD1 H 0.766 . 1 2 854 47 ILE CD1 C 10.039 . 1 3 867 60 ILE HD1 H 0.708 . 1 4 867 60 ILE CD1 C 11.862 . 1 5 876 69 ILE HD1 H 0.671 . 1 6 876 69 ILE CD1 C 12.027 . 1 stop_ save_