data_4357 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR studies of the Pbx1 TALE Homeodomain Protein free in Solution and bound to DNA : Proposal for a Mechanism of HoxB1-Pbx1-DNA Complex Assembly ; _BMRB_accession_number 4357 _BMRB_flat_file_name bmr4357.str _Entry_type original _Submission_date 1999-06-14 _Accession_date 1999-06-18 _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 Jabet Carole . . 2 Gitti Rossitza . . 3 Summers Michael F . 4 Wolberger Cynthia . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 55 "13C chemical shifts" 55 "15N chemical shifts" 55 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 1999-11-30 original author . stop_ _Original_release_date 1999-11-30 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Jabet, C., Gitti, R., Summers, M.F., and Wolberger, C., "NMR studies of the Pbx1 TALE Homeodomain Protein free in Solution and bound to DNA : Proposal for a Mechanism of HoxB1-Pbx1-DNA Complex Assembly", J. Mol. Biol. 291, 521- 530 (1999). ; _Citation_title ; NMR studies of the Pbx1 TALE Homeodomain Protein free in Solution and bound to DNA : Proposal for a Mechanism of HoxB1-Pbx1-DNA Complex Assembly ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 99380399 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Jabet Carole . . 2 Gitti Rossitza . . 3 Summers Michael F . 4 Wolberger Cynthia . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of Molecular Biology' _Journal_volume 291 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 521 _Page_last 530 _Year 1999 _Details . loop_ _Keyword homeodomain Hox Pbx stop_ save_ ################################## # Molecular system description # ################################## save_system_Pbx1-HD-short _Saveframe_category molecular_system _Mol_system_name 'Pbx1 homeodomain' _Abbreviation_common Pbx1-HD-short _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Pbx1-HD-short $Pbx1-HD-short stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'fully reduced' loop_ _Biological_function 'human HOX cofactor' stop_ _Database_query_date . _Details ; Two fragments of the same domain were studied with over 80% of the backbone amide proton, amide nitrogens and alpha carbons assigned. The longest fragment was also complexed with DNA and the same percentage of assignment was achieved. Pbx1 is not complexed with HoxB1. This a NMR study versus a crystal structure ; save_ ######################## # Monomeric polymers # ######################## save_Pbx1-HD-short _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Pbx1 _Abbreviation_common Pbx1 _Molecular_mass . _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 87 _Mol_residue_sequence ; ARRKRRNFNKQATEILNEYF YSHLSNPYPSEEAKEELAKK CGITVSQVSNWFGNKRIRYK KNIGKFQEEANIYAAKTAVT ATNVSAH ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 233 ALA 2 234 ARG 3 235 ARG 4 236 LYS 5 237 ARG 6 238 ARG 7 239 ASN 8 240 PHE 9 241 ASN 10 242 LYS 11 243 GLN 12 244 ALA 13 245 THR 14 246 GLU 15 247 ILE 16 248 LEU 17 249 ASN 18 250 GLU 19 251 TYR 20 252 PHE 21 253 TYR 22 254 SER 23 255 HIS 24 256 LEU 25 257 SER 26 258 ASN 27 259 PRO 28 260 TYR 29 261 PRO 30 262 SER 31 263 GLU 32 264 GLU 33 265 ALA 34 266 LYS 35 267 GLU 36 268 GLU 37 269 LEU 38 270 ALA 39 271 LYS 40 272 LYS 41 273 CYS 42 274 GLY 43 275 ILE 44 276 THR 45 277 VAL 46 278 SER 47 279 GLN 48 280 VAL 49 281 SER 50 282 ASN 51 283 TRP 52 284 PHE 53 285 GLY 54 286 ASN 55 287 LYS 56 288 ARG 57 289 ILE 58 290 ARG 59 291 TYR 60 292 LYS 61 293 LYS 62 294 ASN 63 295 ILE 64 296 GLY 65 297 LYS 66 298 PHE 67 299 GLN 68 300 GLU 69 301 GLU 70 302 ALA 71 303 ASN 72 304 ILE 73 305 TYR 74 306 ALA 75 307 ALA 76 308 LYS 77 309 THR 78 310 ALA 79 311 VAL 80 312 THR 81 313 ALA 82 314 THR 83 315 ASN 84 316 VAL 85 317 SER 86 318 ALA 87 319 HIS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-07-14 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 4358 Pbx1 100.00 87 100.00 100.00 1.82e-55 BMRB 4359 Pbx1 100.00 87 100.00 100.00 1.82e-55 PDB 1B72 "Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX" 100.00 87 100.00 100.00 1.82e-55 PDB 1LFU "Nmr Solution Stucture Of The Extended Pbx Homeodomain Bound To Dna" 93.10 82 98.77 98.77 1.14e-49 PDB 1PUF "Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To Dna" 83.91 73 100.00 100.00 3.51e-45 DBJ BAA96135 "PBX1A [Gallus gallus]" 100.00 430 100.00 100.00 1.26e-48 DBJ BAA96136 "PBX1B [Gallus gallus]" 100.00 347 100.00 100.00 3.90e-54 DBJ BAB83538 "pre-B-cell leukemia transcription factor 1 [Macaca fascicularis]" 100.00 325 98.85 98.85 7.72e-54 DBJ BAF84104 "unnamed protein product [Homo sapiens]" 100.00 430 100.00 100.00 1.60e-48 DBJ BAG10741 "pre-B-cell leukemia transcription factor 1 [synthetic construct]" 100.00 430 100.00 100.00 1.71e-48 GB AAA21832 "homeobox protein [Mus musculus]" 100.00 347 100.00 100.00 2.89e-54 GB AAA36484 "homeobox-containing protein, partial [Homo sapiens]" 100.00 342 100.00 100.00 1.11e-54 GB AAA36764 "E2A/PRL fusion protein, partial [Homo sapiens]" 100.00 550 100.00 100.00 2.92e-50 GB AAA60031 "PBX1a [Homo sapiens]" 100.00 430 100.00 100.00 1.71e-48 GB AAB71191 "PBX1a [Mus musculus]" 100.00 430 100.00 100.00 1.71e-48 PIR B33061 "homeotic protein prl - human" 100.00 342 100.00 100.00 1.11e-54 REF NP_001094151 "pre-B-cell leukemia transcription factor 1 isoform b [Rattus norvegicus]" 100.00 347 100.00 100.00 2.89e-54 REF NP_001128334 "pre-B-cell leukemia transcription factor 1 isoform a [Rattus norvegicus]" 100.00 430 100.00 100.00 1.71e-48 REF NP_001179697 "pre-B-cell leukemia transcription factor 1 [Bos taurus]" 100.00 430 100.00 100.00 1.71e-48 REF NP_001191890 "pre-B-cell leukemia transcription factor 1 isoform 2 [Homo sapiens]" 100.00 347 100.00 100.00 2.89e-54 REF NP_001191892 "pre-B-cell leukemia transcription factor 1 isoform 3 [Homo sapiens]" 100.00 420 100.00 100.00 1.29e-48 SP P40424 "RecName: Full=Pre-B-cell leukemia transcription factor 1; AltName: Full=Homeobox protein PBX1; AltName: Full=Homeobox protein P" 100.00 430 100.00 100.00 1.71e-48 SP P41778 "RecName: Full=Pre-B-cell leukemia transcription factor 1; AltName: Full=Homeobox protein PBX1" 100.00 430 100.00 100.00 1.71e-48 TPG DAA32038 "TPA: pre-B-cell leukemia homeobox 1 [Bos taurus]" 100.00 430 100.00 100.00 1.71e-48 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Gene_mnemonic $Pbx1-HD-short human 9606 Eukaryota Metazoa Homo sapiens Pbx1 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 $Pbx1-HD-short 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_Pbx1-HD_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Pbx1-HD-short 1 mM '[U-90% 15N]' stop_ save_ save_Pbx1-HD_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Pbx1-HD-short 1 mM '[U-90% 15N]' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Task 'data processing' stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Task 'peak assignments' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 800 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-15N_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N NOESY' _Sample_label . save_ save_1H-15N_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N TOCSY' _Sample_label . save_ save_HNCA_3 _Saveframe_category NMR_applied_experiment _Experiment_name HNCA _Sample_label . save_ save_HN(CO)CA_4 _Saveframe_category NMR_applied_experiment _Experiment_name HN(CO)CA _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name HNCA _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name HN(CO)CA _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 0.2 na temperature 298 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 DSS C 13 'methyl protons' ppm 0.0 external indirect . . . 0.251449530 H2O H 1 protons ppm . internal direct . . . . TSP H 1 'methyl protons' ppm 0.0 external indirect . . . . DSS N 15 'methyl protons' ppm 0.0 external 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_assign_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $Pbx1-HD_sample_1 $Pbx1-HD_sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name Pbx1-HD-short _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 . 7 ASN CA C 52.910 . 1 2 . 8 PHE N N 121.196 . 1 3 . 8 PHE H H 8.300 . 1 4 . 8 PHE CA C 57.085 . 1 5 . 9 ASN N N 121.195 . 1 6 . 9 ASN H H 8.340 . 1 7 . 9 ASN CA C 52.853 . 1 8 . 10 LYS N N 121.839 . 1 9 . 10 LYS H H 8.547 . 1 10 . 10 LYS CA C 58.984 . 1 11 . 11 GLN N N 119.563 . 1 12 . 11 GLN H H 8.312 . 1 13 . 11 GLN CA C 58.821 . 1 14 . 12 ALA N N 121.427 . 1 15 . 12 ALA H H 8.106 . 1 16 . 12 ALA CA C 54.720 . 1 17 . 13 THR N N 111.782 . 1 18 . 13 THR H H 7.936 . 1 19 . 13 THR CA C 67.078 . 1 20 . 14 GLU N N 119.770 . 1 21 . 14 GLU H H 7.680 . 1 22 . 14 GLU CA C 58.876 . 1 23 . 15 ILE N N 122.503 . 1 24 . 15 ILE H H 7.726 . 1 25 . 15 ILE CA C 64.859 . 1 26 . 16 LEU N N 122.203 . 1 27 . 16 LEU H H 8.063 . 1 28 . 16 LEU CA C 58.027 . 1 29 . 17 ASN N N 118.503 . 1 30 . 17 ASN H H 8.442 . 1 31 . 17 ASN CA C 56.178 . 1 32 . 18 GLU N N 119.866 . 1 33 . 18 GLU H H 8.188 . 1 34 . 18 GLU CA C 59.768 . 1 35 . 19 TYR N N 120.131 . 1 36 . 19 TYR H H 7.936 . 1 37 . 19 TYR CA C 62.379 . 1 38 . 20 PHE N N 122.277 . 1 39 . 20 PHE H H 9.439 . 1 40 . 20 PHE CA C 63.237 . 1 41 . 21 TYR N N 112.665 . 1 42 . 21 TYR H H 8.775 . 1 43 . 21 TYR CA C 61.967 . 1 44 . 22 SER N N 112.205 . 1 45 . 22 SER H H 7.621 . 1 46 . 22 SER CA C 58.917 . 1 47 . 23 HIS N N 120.948 . 1 48 . 23 HIS H H 7.451 . 1 49 . 23 HIS CA C 55.453 . 1 50 . 24 LEU N N 120.951 . 1 51 . 24 LEU H H 7.382 . 1 52 . 24 LEU CA C 57.482 . 1 53 . 25 SER N N 110.692 . 1 54 . 25 SER H H 8.133 . 1 55 . 25 SER CA C 59.590 . 1 56 . 26 ASN N N 115.704 . 1 57 . 26 ASN H H 7.510 . 1 58 . 26 ASN CA C 51.703 . 1 59 . 29 PRO CA C 61.850 . 1 60 . 30 SER N N 118.055 . 1 61 . 30 SER H H 8.311 . 1 62 . 30 SER CA C 56.951 . 1 63 . 31 GLU N N 120.414 . 1 64 . 31 GLU H H 8.964 . 1 65 . 31 GLU CA C 59.878 . 1 66 . 32 GLU N N 118.658 . 1 67 . 32 GLU H H 8.710 . 1 68 . 32 GLU CA C 59.732 . 1 69 . 33 ALA N N 124.283 . 1 70 . 33 ALA H H 7.913 . 1 71 . 33 ALA CA C 54.619 . 1 72 . 34 LYS N N 117.074 . 1 73 . 34 LYS H H 8.461 . 1 74 . 34 LYS CA C 60.625 . 1 75 . 35 GLU N N 119.180 . 1 76 . 35 GLU H H 8.000 . 1 77 . 35 GLU CA C 59.213 . 1 78 . 36 GLU N N 120.408 . 1 79 . 36 GLU H H 7.662 . 1 80 . 36 GLU CA C 59.026 . 1 81 . 37 LEU N N 119.940 . 1 82 . 37 LEU H H 8.253 . 1 83 . 37 LEU CA C 57.608 . 1 84 . 38 ALA N N 123.052 . 1 85 . 38 ALA H H 8.650 . 1 86 . 38 ALA CA C 55.749 . 1 87 . 39 LYS N N 116.938 . 1 88 . 39 LYS H H 7.644 . 1 89 . 39 LYS CA C 59.823 . 1 90 . 40 LYS N N 118.846 . 1 91 . 40 LYS H H 8.006 . 1 92 . 40 LYS CA C 59.134 . 1 93 . 41 CYS N N 112.784 . 1 94 . 41 CYS H H 8.090 . 1 95 . 41 CYS CA C 60.928 . 1 96 . 42 GLY N N 109.721 . 1 97 . 42 GLY H H 7.927 . 1 98 . 42 GLY CA C 46.433 . 1 99 . 43 ILE N N 112.245 . 1 100 . 43 ILE H H 7.682 . 1 101 . 43 ILE CA C 58.917 . 1 102 . 44 THR N N 108.294 . 1 103 . 44 THR H H 8.214 . 1 104 . 44 THR CA C 60.196 . 1 105 . 45 VAL N N 120.743 . 1 106 . 45 VAL H H 8.944 . 1 107 . 45 VAL CA C 67.034 . 1 108 . 46 SER N N 115.688 . 1 109 . 46 SER H H 8.367 . 1 110 . 46 SER CA C 61.446 . 1 111 . 47 GLN N N 121.543 . 1 112 . 47 GLN H H 7.815 . 1 113 . 47 GLN CA C 59.259 . 1 114 . 48 VAL N N 121.939 . 1 115 . 48 VAL H H 8.223 . 1 116 . 48 VAL CA C 67.424 . 1 117 . 49 SER N N 115.951 . 1 118 . 49 SER H H 8.989 . 1 119 . 49 SER CA C 62.478 . 1 120 . 50 ASN N N 121.120 . 1 121 . 50 ASN H H 8.601 . 1 122 . 50 ASN CA C 55.897 . 1 123 . 51 TRP N N 122.755 . 1 124 . 51 TRP H H 8.460 . 1 125 . 51 TRP CA C 62.502 . 1 126 . 51 TRP NE1 N 128.871 . 1 127 . 51 TRP HE1 H 9.956 . 1 128 . 52 PHE N N 118.123 . 1 129 . 52 PHE H H 8.741 . 1 130 . 52 PHE CA C 63.345 . 1 131 . 53 GLY N N 106.168 . 1 132 . 53 GLY H H 8.251 . 1 133 . 53 GLY CA C 47.339 . 1 134 . 54 ASN N N 118.619 . 1 135 . 54 ASN H H 7.563 . 1 136 . 54 ASN CA C 55.373 . 1 137 . 55 LYS N N 122.384 . 1 138 . 55 LYS H H 8.034 . 1 139 . 55 LYS CA C 56.777 . 1 140 . 56 ARG N N 115.965 . 1 141 . 56 ARG H H 8.090 . 1 142 . 56 ARG CA C 60.226 . 1 143 . 57 ILE N N 117.790 . 1 144 . 57 ILE H H 7.082 . 1 145 . 57 ILE CA C 63.883 . 1 146 . 58 ARG N N 120.451 . 1 147 . 58 ARG H H 7.780 . 1 148 . 58 ARG CA C 58.274 . 1 149 . 59 TYR N N 120.138 . 1 150 . 59 TYR H H 8.484 . 1 151 . 59 TYR CA C 60.797 . 1 152 . 60 LYS N N 119.336 . 1 153 . 60 LYS H H 7.730 . 1 154 . 61 LYS N N 119.685 . 1 155 . 61 LYS H H 7.886 . 1 156 . 61 LYS CA C 57.537 . 1 157 . 62 ASN N N 118.544 . 1 158 . 62 ASN H H 8.149 . 1 159 . 62 ASN CA C 53.898 . 1 160 . 63 ILE N N 117.845 . 1 161 . 63 ILE H H 7.867 . 1 162 . 63 ILE CA C 61.204 . 1 163 . 64 GLY N N 117.079 . 1 164 . 64 GLY H H 7.724 . 1 165 . 64 GLY CA C 46.053 . 1 stop_ save_