data_11374 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1 with RNA (CCCCC) ; _BMRB_accession_number 11374 _BMRB_flat_file_name bmr11374.str _Entry_type original _Submission_date 2010-09-08 _Accession_date 2010-09-08 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Takahashi M. . . 2 Kuwasako K. . . 3 Abe C. . . 4 Tsuda K. . . 5 Inoue M. . . 6 Terada T. . . 7 Shirouzu M. . . 8 Kobayashi N. . . 9 Kigawa T. . . 10 Taguchi S. . . 11 Guntert P. . . 12 Hayashizaki Y. . . 13 Tanaka A. . . 14 Muto Y. . . 15 Yokoyama S. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 96 "15N chemical shifts" 96 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-11-30 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 11370 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1, C terminal truncated' 11371 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1, D131A mutant' 11372 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1, K138A mutant' 11373 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1, T134A mutant' 11375 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1 with RNA (UUUUU)' 11376 'Assigned chemical shifts of the second RNA recognition motif (RRM) of TIA-1' stop_ _Original_release_date 2010-11-30 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18500819 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kuwasako Kanako . . 2 Takahashi Mari . . 3 Tochio Naoya . . 4 Abe Chikage . . 5 Tsuda Kengo . . 6 Inoue Makoto . . 7 Terada Takaho . . 8 Shirouzu Mikako . . 9 Kobayashi Naohiro . . 10 Kigawa Takanori . . 11 Taguchi Seiichi . . 12 Tanaka Akiko . . 13 Hayashizaki Yoshihide . . 14 Guntert Peter . . 15 Muto Yutaka . . 16 Yokoyama Shigeyuki . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 47 _Journal_issue 24 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6437 _Page_last 6450 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Tia1 protein' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RRM domain' $entity_1 'RNA (CCCCC)' $entity_2 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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'RRM domain' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 115 _Mol_residue_sequence ; GSSGSSGQKKDTSNHFHVFV GDLSPEITTEDIKAAFAPFG RISDARVVKDMATGKSKGYG FVSFFNKWDAENAIQQMGGQ WLGGRQIRTNWATRKPPAPK STYESNTKQSGPSSG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 . GLY 2 . SER 3 . SER 4 . GLY 5 . SER 6 . SER 7 . GLY 8 . GLN 9 3 LYS 10 4 LYS 11 5 ASP 12 6 THR 13 7 SER 14 8 ASN 15 9 HIS 16 10 PHE 17 11 HIS 18 12 VAL 19 13 PHE 20 14 VAL 21 15 GLY 22 16 ASP 23 17 LEU 24 18 SER 25 19 PRO 26 20 GLU 27 21 ILE 28 22 THR 29 23 THR 30 24 GLU 31 25 ASP 32 26 ILE 33 27 LYS 34 28 ALA 35 29 ALA 36 30 PHE 37 31 ALA 38 32 PRO 39 33 PHE 40 34 GLY 41 35 ARG 42 36 ILE 43 37 SER 44 38 ASP 45 39 ALA 46 40 ARG 47 41 VAL 48 42 VAL 49 43 LYS 50 44 ASP 51 45 MET 52 46 ALA 53 47 THR 54 48 GLY 55 49 LYS 56 50 SER 57 51 LYS 58 52 GLY 59 53 TYR 60 54 GLY 61 55 PHE 62 56 VAL 63 57 SER 64 58 PHE 65 59 PHE 66 60 ASN 67 61 LYS 68 62 TRP 69 63 ASP 70 64 ALA 71 65 GLU 72 66 ASN 73 67 ALA 74 68 ILE 75 69 GLN 76 70 GLN 77 71 MET 78 72 GLY 79 73 GLY 80 74 GLN 81 75 TRP 82 76 LEU 83 77 GLY 84 78 GLY 85 79 ARG 86 80 GLN 87 81 ILE 88 82 ARG 89 83 THR 90 84 ASN 91 85 TRP 92 86 ALA 93 87 THR 94 88 ARG 95 89 LYS 96 90 PRO 97 91 PRO 98 92 ALA 99 93 PRO 100 94 LYS 101 95 SER 102 96 THR 103 97 TYR 104 98 GLU 105 99 SER 106 100 ASN 107 101 THR 108 102 LYS 109 103 GLN 110 104 SER 111 105 GLY 112 106 PRO 113 107 SER 114 108 SER 115 109 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-07 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 11370 "RRM domain C terminal truncated" 75.65 87 100.00 100.00 7.29e-57 BMRB 11371 "RRM domain D131A mutant" 89.57 103 99.03 99.03 2.39e-68 BMRB 11372 "RRM domain K138A mutant" 89.57 103 99.03 99.03 1.01e-68 BMRB 11373 "RRM domain T134A mutant" 89.57 103 99.03 99.03 8.77e-69 BMRB 11375 "RRM domain" 100.00 115 100.00 100.00 2.81e-77 BMRB 11376 "RRM domain" 100.00 115 100.00 100.00 2.81e-77 PDB 2DGO "Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1" 100.00 115 100.00 100.00 2.81e-77 PDB 2RNE "Solution Structure Of The Second Rna Recognition Motif (Rrm) Of Tia-1" 100.00 115 100.00 100.00 2.81e-77 GB EAW99825 "TIA1 cytotoxic granule-associated RNA binding protein, isoform CRA_c, partial [Homo sapiens]" 90.43 144 99.04 99.04 2.21e-69 REF XP_005430921 "PREDICTED: nucleolysin TIA-1 isoform p40 [Geospiza fortis]" 90.43 367 98.08 99.04 6.94e-66 stop_ save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'RNA (CCCCC)' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 5 _Mol_residue_sequence CCCCC loop_ _Residue_seq_code _Residue_label 1 C 2 C 3 C 4 C 5 C 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 $entity_1 Mouse 10090 Eukaryota Metazoa Mus musculus 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 $entity_1 'cell free synthesis' 'E. coli' Escherichia coli . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 0.2mM RNA, 20mM [U-99% 2H] TRIS, 100mM sodium chloride, 1mM [U-98% 2H] DTT, 0.02% sodium azide, 1mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM '[U-99% 13C; U-99% 15N]' $entity_2 0.2 mM 'natural abundance' TRIS 20 mM '[U-99% 2H]' 'sodium chloride' 100 mM 'natural abundance' DTT 1 mM '[U-98% 2H]' 'sodium azide' 0.02 % 'natural abundance' H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_OPAL _Saveframe_category software _Name OPAL _Version . loop_ _Vendor _Address _Electronic_address 'Luginbuhl, Guntert, Billeter and Wuthrich' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_3D_1H-15N_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_1 save_ save_3D_1H-13C_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 100 0.1 mM pH 7.0 0.05 pH pressure 1 0.001 atm temperature 298 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_reference_1 _Saveframe_category chemical_shift_reference _Details ; Chemical shift reference of 1H was based on the proton of water (4.784ppm at 298K) and then those of 15N and 13C were calculated based on their gyromagnetic ratios. ; 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 DSS C 13 'methyl protons' ppm 0.0 . indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.0 . indirect . . . 1.0 DSS N 15 'methyl protons' ppm 0.0 . indirect . . . 0.101329118 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_chemical_shift_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $OPAL stop_ loop_ _Experiment_label '3D 1H-15N NOESY' '3D 1H-13C NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $reference_1 _Mol_system_component_name 'RRM domain' _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 3 9 LYS H H 8.535 0.030 1 2 3 9 LYS N N 123.849 0.300 1 3 4 10 LYS H H 8.459 0.030 1 4 4 10 LYS N N 123.658 0.300 1 5 5 11 ASP H H 8.448 0.030 1 6 5 11 ASP N N 122.345 0.300 1 7 6 12 THR H H 8.220 0.030 1 8 6 12 THR N N 114.842 0.300 1 9 7 13 SER H H 8.317 0.030 1 10 7 13 SER N N 118.883 0.300 1 11 8 14 ASN H H 8.262 0.030 1 12 8 14 ASN N N 119.331 0.300 1 13 9 15 HIS H H 7.373 0.030 1 14 9 15 HIS N N 119.153 0.300 1 15 10 16 PHE H H 8.390 0.030 1 16 10 16 PHE N N 117.347 0.300 1 17 11 17 HIS H H 8.920 0.030 1 18 11 17 HIS N N 124.353 0.300 1 19 12 18 VAL H H 9.818 0.030 1 20 12 18 VAL N N 126.932 0.300 1 21 13 19 PHE H H 9.123 0.030 1 22 13 19 PHE N N 128.213 0.300 1 23 14 20 VAL H H 7.681 0.030 1 24 14 20 VAL N N 126.893 0.300 1 25 15 21 GLY H H 8.654 0.030 1 26 15 21 GLY N N 111.045 0.300 1 27 16 22 ASP H H 8.378 0.030 1 28 16 22 ASP N N 115.636 0.300 1 29 17 23 LEU H H 7.597 0.030 1 30 17 23 LEU N N 112.377 0.300 1 31 18 24 SER H H 8.935 0.030 1 32 18 24 SER N N 120.901 0.300 1 33 20 26 GLU H H 9.009 0.030 1 34 20 26 GLU N N 116.129 0.300 1 35 21 27 ILE H H 7.351 0.030 1 36 21 27 ILE N N 121.706 0.300 1 37 22 28 THR H H 9.403 0.030 1 38 22 28 THR N N 121.223 0.300 1 39 23 29 THR H H 9.032 0.030 1 40 23 29 THR N N 118.411 0.300 1 41 24 30 GLU H H 8.411 0.030 1 42 24 30 GLU N N 119.940 0.300 1 43 25 31 ASP H H 7.703 0.030 1 44 25 31 ASP N N 120.100 0.300 1 45 26 32 ILE H H 7.916 0.030 1 46 26 32 ILE N N 118.520 0.300 1 47 27 33 LYS H H 8.290 0.030 1 48 27 33 LYS N N 121.653 0.300 1 49 28 34 ALA H H 7.744 0.030 1 50 28 34 ALA N N 118.243 0.300 1 51 29 35 ALA H H 7.833 0.030 1 52 29 35 ALA N N 118.034 0.300 1 53 30 36 PHE H H 7.974 0.030 1 54 30 36 PHE N N 112.056 0.300 1 55 31 37 ALA H H 8.043 0.030 1 56 31 37 ALA N N 125.049 0.300 1 57 33 39 PHE H H 7.692 0.030 1 58 33 39 PHE N N 112.696 0.300 1 59 34 40 GLY H H 7.601 0.030 1 60 34 40 GLY N N 104.647 0.300 1 61 35 41 ARG H H 8.237 0.030 1 62 35 41 ARG N N 116.988 0.300 1 63 36 42 ILE H H 8.508 0.030 1 64 36 42 ILE N N 128.034 0.300 1 65 37 43 SER H H 8.838 0.030 1 66 37 43 SER N N 123.297 0.300 1 67 38 44 ASP H H 7.267 0.030 1 68 38 44 ASP N N 119.641 0.300 1 69 39 45 ALA H H 7.984 0.030 1 70 39 45 ALA N N 121.317 0.300 1 71 40 46 ARG H H 8.735 0.030 1 72 40 46 ARG N N 115.328 0.300 1 73 41 47 VAL H H 7.608 0.030 1 74 41 47 VAL N N 123.242 0.300 1 75 42 48 VAL H H 8.388 0.030 1 76 42 48 VAL N N 130.306 0.300 1 77 43 49 LYS H H 8.165 0.030 1 78 43 49 LYS N N 125.241 0.300 1 79 44 50 ASP H H 8.644 0.030 1 80 44 50 ASP N N 121.838 0.300 1 81 45 51 MET H H 9.061 0.030 1 82 45 51 MET N N 127.283 0.300 1 83 46 52 ALA H H 8.559 0.030 1 84 46 52 ALA N N 120.754 0.300 1 85 47 53 THR H H 7.756 0.030 1 86 47 53 THR N N 104.923 0.300 1 87 48 54 GLY H H 8.451 0.030 1 88 48 54 GLY N N 111.463 0.300 1 89 49 55 LYS H H 7.701 0.030 1 90 49 55 LYS N N 119.242 0.300 1 91 50 56 SER H H 8.761 0.030 1 92 50 56 SER N N 115.540 0.300 1 93 51 57 LYS H H 9.294 0.030 1 94 51 57 LYS N N 125.916 0.300 1 95 52 58 GLY H H 9.159 0.030 1 96 52 58 GLY N N 106.718 0.300 1 97 53 59 TYR H H 6.977 0.030 1 98 53 59 TYR N N 112.875 0.300 1 99 54 60 GLY H H 8.787 0.030 1 100 54 60 GLY N N 106.234 0.300 1 101 55 61 PHE H H 8.459 0.030 1 102 55 61 PHE N N 113.453 0.300 1 103 56 62 VAL H H 8.932 0.030 1 104 56 62 VAL N N 120.167 0.300 1 105 57 63 SER H H 8.770 0.030 1 106 57 63 SER N N 122.337 0.300 1 107 58 64 PHE H H 9.263 0.030 1 108 58 64 PHE N N 121.902 0.300 1 109 59 65 PHE H H 7.703 0.030 1 110 59 65 PHE N N 117.991 0.300 1 111 60 66 ASN H H 8.667 0.030 1 112 60 66 ASN N N 114.221 0.300 1 113 61 67 LYS H H 8.165 0.030 1 114 61 67 LYS N N 126.726 0.300 1 115 62 68 TRP H H 7.571 0.030 1 116 62 68 TRP N N 116.532 0.300 1 117 63 69 ASP H H 6.859 0.030 1 118 63 69 ASP N N 121.274 0.300 1 119 64 70 ALA H H 6.597 0.030 1 120 64 70 ALA N N 119.724 0.300 1 121 65 71 GLU H H 8.322 0.030 1 122 65 71 GLU N N 117.200 0.300 1 123 66 72 ASN H H 7.917 0.030 1 124 66 72 ASN N N 117.876 0.300 1 125 67 73 ALA H H 7.877 0.030 1 126 67 73 ALA N N 121.655 0.300 1 127 68 74 ILE H H 8.072 0.030 1 128 68 74 ILE N N 116.524 0.300 1 129 69 75 GLN H H 7.623 0.030 1 130 69 75 GLN N N 117.094 0.300 1 131 70 76 GLN H H 8.427 0.030 1 132 70 76 GLN N N 114.692 0.300 1 133 71 77 MET H H 7.681 0.030 1 134 71 77 MET N N 113.167 0.300 1 135 72 78 GLY H H 7.029 0.030 1 136 72 78 GLY N N 106.996 0.300 1 137 73 79 GLY H H 8.441 0.030 1 138 73 79 GLY N N 115.358 0.300 1 139 74 80 GLN H H 7.605 0.030 1 140 74 80 GLN N N 119.082 0.300 1 141 75 81 TRP H H 8.627 0.030 1 142 75 81 TRP N N 121.002 0.300 1 143 76 82 LEU H H 8.558 0.030 1 144 76 82 LEU N N 125.924 0.300 1 145 77 83 GLY H H 9.317 0.030 1 146 77 83 GLY N N 115.393 0.300 1 147 78 84 GLY H H 8.734 0.030 1 148 78 84 GLY N N 107.802 0.300 1 149 79 85 ARG H H 7.620 0.030 1 150 79 85 ARG N N 118.518 0.300 1 151 80 86 GLN H H 7.801 0.030 1 152 80 86 GLN N N 121.787 0.300 1 153 81 87 ILE H H 8.129 0.030 1 154 81 87 ILE N N 118.085 0.300 1 155 82 88 ARG H H 7.920 0.030 1 156 82 88 ARG N N 119.782 0.300 1 157 83 89 THR H H 8.377 0.030 1 158 83 89 THR N N 110.727 0.300 1 159 84 90 ASN H H 8.687 0.030 1 160 84 90 ASN N N 115.821 0.300 1 161 85 91 TRP H H 8.810 0.030 1 162 85 91 TRP N N 122.277 0.300 1 163 86 92 ALA H H 8.988 0.030 1 164 86 92 ALA N N 126.787 0.300 1 165 87 93 THR H H 8.563 0.030 1 166 87 93 THR N N 114.859 0.300 1 167 88 94 ARG H H 8.360 0.030 1 168 88 94 ARG N N 123.611 0.300 1 169 89 95 LYS H H 8.229 0.030 1 170 89 95 LYS N N 123.713 0.300 1 171 92 98 ALA H H 8.290 0.030 1 172 92 98 ALA N N 125.533 0.300 1 173 94 100 LYS H H 8.414 0.030 1 174 94 100 LYS N N 121.743 0.300 1 175 95 101 SER H H 8.364 0.030 1 176 95 101 SER N N 117.060 0.300 1 177 96 102 THR H H 8.133 0.030 1 178 96 102 THR N N 115.589 0.300 1 179 97 103 TYR H H 8.123 0.030 1 180 97 103 TYR N N 121.852 0.300 1 181 98 104 GLU H H 8.220 0.030 1 182 98 104 GLU N N 122.672 0.300 1 183 99 105 SER H H 8.279 0.030 1 184 99 105 SER N N 116.780 0.300 1 185 100 106 ASN H H 8.476 0.030 1 186 100 106 ASN N N 120.902 0.300 1 187 101 107 THR H H 8.065 0.030 1 188 101 107 THR N N 114.288 0.300 1 189 102 108 LYS H H 8.279 0.030 1 190 102 108 LYS N N 124.426 0.300 1 191 103 109 GLN H H 8.013 0.030 1 192 103 109 GLN N N 127.272 0.300 1 stop_ save_