data_9500 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of actin-interacting domain of troponin ; _BMRB_accession_number 9500 _BMRB_flat_file_name bmr9500.str _Entry_type original _Submission_date 2005-11-18 _Accession_date 2005-11-18 _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 Murakami Kenji . . 2 Yumoto Fumiaki . . 3 Ohki Shin-ya . . 4 Yasunaga Takuo . . 5 Tanokura Masaru . . 6 Wakabayashi Takeyuki . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 48 "13C chemical shifts" 92 "15N chemical shifts" 48 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-05-21 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 10012 'Assigned chemical shift of actin-binding domain of troponin in Ca2+-free state' stop_ _Original_release_date 2009-05-21 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural Basis for Ca(2+)-regulated Muscle Relaxation at Interaction Sites of Troponin with Actin and Tropomyosin ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16061251 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Murakami Kenji . . 2 Yumoto Fumiaki . . 3 Ohki Shin-ya . . 4 Yasunaga Takuo . . 5 Tanokura Masaru . . 6 Wakabayashi Takeyuki . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 352 _Journal_issue 1 _Journal_ASTM JMOBAK _Journal_ISSN 0022-2836 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 178 _Page_last 201 _Year 2005 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'troponin complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Troponin I' $TnI 'CALCIUM ION' $CA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state 'protein-protein complex' _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_TnI _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common TnI _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 52 _Mol_residue_sequence ; KVNMDLRANLKQVKKEDTEK EKDLRDVGDWRKNIEEKSGM EGRKKMFEAGES ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 131 LYS 2 132 VAL 3 133 ASN 4 134 MET 5 135 ASP 6 136 LEU 7 137 ARG 8 138 ALA 9 139 ASN 10 140 LEU 11 141 LYS 12 142 GLN 13 143 VAL 14 144 LYS 15 145 LYS 16 146 GLU 17 147 ASP 18 148 THR 19 149 GLU 20 150 LYS 21 151 GLU 22 152 LYS 23 153 ASP 24 154 LEU 25 155 ARG 26 156 ASP 27 157 VAL 28 158 GLY 29 159 ASP 30 160 TRP 31 161 ARG 32 162 LYS 33 163 ASN 34 164 ILE 35 165 GLU 36 166 GLU 37 167 LYS 38 168 SER 39 169 GLY 40 170 MET 41 171 GLU 42 172 GLY 43 173 ARG 44 174 LYS 45 175 LYS 46 176 MET 47 177 PHE 48 178 GLU 49 179 ALA 50 180 GLY 51 181 GLU 52 182 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-28 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 10012 TnI 100.00 52 100.00 100.00 2.36e-26 PDB 1VDI "Solution Structure Of Actin-Binding Domain Of Troponin In Ca2+-Free State" 100.00 52 100.00 100.00 2.36e-26 PDB 1VDJ "Solution Structure Of Actin-Binding Domain Of Troponin In Ca2+-Bound State" 100.00 52 100.00 100.00 2.36e-26 PDB 1YTZ "Crystal Structure Of Skeletal Muscle Troponin In The Ca2+- Activated State" 100.00 182 100.00 100.00 1.60e-26 EMBL CAA27447 "sTnI protein (aa 85-182), partial [Gallus gallus]" 100.00 98 100.00 100.00 2.07e-26 GB AAA61952 "troponin I [Gallus gallus]" 100.00 183 100.00 100.00 1.94e-26 GB AAB00122 "troponin I [Coturnix coturnix]" 100.00 183 100.00 100.00 1.94e-26 GB ACU12238 "troponin I, partial [Alectoris rufa]" 88.46 67 100.00 100.00 7.45e-22 GB ACU12239 "troponin I, partial [Alectoris chukar]" 88.46 67 100.00 100.00 7.45e-22 GB EMC88037 "Troponin I, fast skeletal muscle, partial [Columba livia]" 100.00 178 100.00 100.00 1.70e-26 REF NP_990748 "troponin I, fast skeletal muscle [Gallus gallus]" 100.00 183 100.00 100.00 1.94e-26 REF XP_002199061 "PREDICTED: troponin I, fast skeletal muscle [Taeniopygia guttata]" 100.00 183 98.08 98.08 1.92e-25 REF XP_003206335 "PREDICTED: troponin I, fast skeletal muscle [Meleagris gallopavo]" 100.00 183 100.00 100.00 1.92e-26 REF XP_003206336 "PREDICTED: troponin I, fast skeletal muscle [Meleagris gallopavo]" 100.00 183 100.00 100.00 1.92e-26 REF XP_005019797 "PREDICTED: troponin I, fast skeletal muscle isoform X1 [Anas platyrhynchos]" 100.00 186 98.08 98.08 3.17e-25 SP P68246 "RecName: Full=Troponin I, fast skeletal muscle; AltName: Full=Troponin I, fast-twitch isoform [Gallus gallus]" 100.00 183 100.00 100.00 1.94e-26 SP P68247 "RecName: Full=Troponin I, fast skeletal muscle; AltName: Full=Troponin I, fast-twitch isoform [Coturnix japonica]" 100.00 183 100.00 100.00 1.94e-26 stop_ save_ ############# # Ligands # ############# save_CA _Saveframe_category ligand _Mol_type non-polymer _Name_common CA _Molecular_mass . _Details . _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $TnI chicken 9031 Eukaryota Metazoa Gallus gallus 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 $TnI 'recombinant technology' . Escherichia coli . pET3a stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'The troponin ternary complex high Ca2+' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $assembly . mM 0.8 1.2 '[U-13C; U-15N]' $assembly . mM 0.8 1.2 'natural abundance' $assembly . mM 0.8 1.2 'natural abundance' KCl 240 mM . . . NaHCO3 0.3 mM . . . MgCl2 3 mM . . . $CA 0.1 mM . . . H2O 90 % . . . D2O 10 % . . . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'The troponin ternary complex high Ca2+' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $assembly . mM 0.8 1.2 '[U-13C; U-15N]' $assembly . mM 0.8 1.2 'natural abundance' $assembly . mM 0.8 1.2 'natural abundance' KCl 240 mM . . . NaHCO3 0.3 mM . . . MgCl2 3 mM . . . $CA 0.1 mM . . . D2O 100 % . . . stop_ save_ ############################ # Computer software used # ############################ 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_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 750 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_HNCACB_1 _Saveframe_category NMR_applied_experiment _Experiment_name HNCACB _Sample_label $sample_1 save_ save_CBCA(CO)NH_2 _Saveframe_category NMR_applied_experiment _Experiment_name CBCA(CO)NH _Sample_label $sample_1 save_ save_HNCA_3 _Saveframe_category NMR_applied_experiment _Experiment_name HNCA _Sample_label $sample_1 save_ save_HN(CO)CA_4 _Saveframe_category NMR_applied_experiment _Experiment_name HN(CO)CA _Sample_label $sample_1 save_ save_HNCO_5 _Saveframe_category NMR_applied_experiment _Experiment_name HNCO _Sample_label $sample_1 save_ save_H(CCO)NH_6 _Saveframe_category NMR_applied_experiment _Experiment_name H(CCO)NH _Sample_label $sample_1 save_ save_C(CO)NH_7 _Saveframe_category NMR_applied_experiment _Experiment_name C(CO)NH _Sample_label $sample_1 save_ save_HCCH-TOCSY_8 _Saveframe_category NMR_applied_experiment _Experiment_name HCCH-TOCSY _Sample_label $sample_1 save_ save_2D_13C-NOESY_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-NOESY' _Sample_label $sample_1 save_ save_2D_aromatic_13C-edited_NOESY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D aromatic 13C-edited NOESY' _Sample_label $sample_2 save_ save_3D_13C-edited_NOESY_11 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 13C-edited NOESY' _Sample_label $sample_1 save_ save_3D_15N-edited_NOESY_12 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N-edited 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 pH 7 . pH temperature 298 . 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 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 na indirect . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na 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_shifts_wCa _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label HNCACB CBCA(CO)NH HNCA HN(CO)CA HNCO H(CCO)NH C(CO)NH HCCH-TOCSY '2D 13C-NOESY' '2D aromatic 13C-edited NOESY' '3D 13C-edited NOESY' '3D 15N-edited NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'Troponin I' _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 1 134 4 MET H H 8.513 . 1 2 134 4 MET N N 120.6 . 1 3 135 5 ASP CA C 55.8 . 1 4 135 5 ASP CB C 41.3 . 1 5 136 6 LEU H H 8.402 . 1 6 136 6 LEU CA C 55.8 . 1 7 136 6 LEU CB C 41.3 . 1 8 136 6 LEU N N 119.5 . 1 9 137 7 ARG H H 8.374 . 1 10 137 7 ARG CA C 56.83 . 1 11 137 7 ARG CB C 30.3 . 1 12 137 7 ARG N N 119.7 . 1 13 138 8 ALA H H 8.098 . 1 14 138 8 ALA CA C 53.2 . 1 15 138 8 ALA CB C 19.45 . 1 16 138 8 ALA N N 123 . 1 17 139 9 ASN H H 8.26 . 1 18 139 9 ASN CA C 53.51 . 1 19 139 9 ASN CB C 38.83 . 1 20 139 9 ASN N N 116.8 . 1 21 140 10 LEU H H 8.057 . 1 22 140 10 LEU CA C 55.46 . 1 23 140 10 LEU CB C 42.24 . 1 24 140 10 LEU N N 121.6 . 1 25 141 11 LYS H H 8.151 . 1 26 141 11 LYS CA C 56.59 . 1 27 141 11 LYS CB C 32.92 . 1 28 141 11 LYS N N 121 . 1 29 142 12 GLN H H 8.255 . 1 30 142 12 GLN CA C 55.8 . 1 31 142 12 GLN CB C 29.6 . 1 32 142 12 GLN N N 121.3 . 1 33 143 13 VAL H H 8.188 . 1 34 143 13 VAL CA C 62.38 . 1 35 143 13 VAL CB C 32.89 . 1 36 143 13 VAL N N 122.1 . 1 37 144 14 LYS H H 8.451 . 1 38 144 14 LYS CA C 56.06 . 1 39 144 14 LYS CB C 33.34 . 1 40 144 14 LYS N N 125.9 . 1 41 145 15 LYS H H 8.483 . 1 42 145 15 LYS CA C 56.58 . 1 43 145 15 LYS CB C 33.33 . 1 44 145 15 LYS N N 124.4 . 1 45 146 16 GLU H H 8.657 . 1 46 146 16 GLU CA C 56.7 . 1 47 146 16 GLU CB C 30.52 . 1 48 146 16 GLU N N 122.2 . 1 49 147 17 ASP H H 8.463 . 1 50 147 17 ASP CA C 54.66 . 1 51 147 17 ASP CB C 41.21 . 1 52 147 17 ASP N N 121.8 . 1 53 148 18 THR H H 8.115 . 1 54 148 18 THR CA C 62.36 . 1 55 148 18 THR CB C 69.55 . 1 56 148 18 THR N N 113.9 . 1 57 149 19 GLU H H 8.406 . 1 58 149 19 GLU CA C 57.02 . 1 59 149 19 GLU CB C 30.18 . 1 60 149 19 GLU N N 122.8 . 1 61 150 20 LYS H H 8.181 . 1 62 150 20 LYS CA C 56.8 . 1 63 150 20 LYS CB C 33.13 . 1 64 150 20 LYS N N 121.7 . 1 65 151 21 GLU H H 8.377 . 1 66 151 21 GLU CA C 56.99 . 1 67 151 21 GLU CB C 30.13 . 1 68 151 21 GLU N N 121.3 . 1 69 152 22 LYS H H 8.22 . 1 70 152 22 LYS CA C 56.88 . 1 71 152 22 LYS CB C 33.23 . 1 72 152 22 LYS N N 121.7 . 1 73 153 23 ASP H H 8.354 . 1 74 153 23 ASP CA C 54.45 . 1 75 153 23 ASP CB C 41.4 . 1 76 153 23 ASP N N 121.2 . 1 77 154 24 LEU H H 8.188 . 1 78 154 24 LEU CA C 55.5 . 1 79 154 24 LEU CB C 42.06 . 1 80 154 24 LEU N N 123 . 1 81 155 25 ARG H H 8.241 . 1 82 155 25 ARG CA C 56.63 . 1 83 155 25 ARG CB C 30.82 . 1 84 155 25 ARG N N 120.7 . 1 85 156 26 ASP H H 8.331 . 1 86 156 26 ASP CA C 54.39 . 1 87 156 26 ASP CB C 41.4 . 1 88 156 26 ASP N N 120.9 . 1 89 157 27 VAL H H 8.043 . 1 90 157 27 VAL CA C 62.51 . 1 91 157 27 VAL CB C 32.66 . 1 92 157 27 VAL N N 119.4 . 1 93 158 28 GLY H H 8.405 . 1 94 158 28 GLY CA C 45.56 . 1 95 158 28 GLY N N 111.1 . 1 96 159 29 ASP H H 8.213 . 1 97 159 29 ASP CA C 54.45 . 1 98 159 29 ASP CB C 41.07 . 1 99 159 29 ASP N N 121 . 1 100 160 30 TRP H H 7.979 . 1 101 160 30 TRP CA C 57.93 . 1 102 160 30 TRP CB C 29 . 1 103 160 30 TRP N N 122 . 1 104 161 31 ARG H H 7.786 . 1 105 161 31 ARG CA C 56.96 . 1 106 161 31 ARG CB C 30.23 . 1 107 161 31 ARG N N 121.4 . 1 108 162 32 LYS H H 7.885 . 1 109 162 32 LYS CA C 56.79 . 1 110 162 32 LYS CB C 32.97 . 1 111 162 32 LYS N N 120.4 . 1 112 163 33 ASN H H 8.252 . 1 113 163 33 ASN CA C 53.62 . 1 114 163 33 ASN CB C 38.84 . 1 115 163 33 ASN N N 118.8 . 1 116 164 34 ILE H H 7.974 . 1 117 164 34 ILE CA C 61.66 . 1 118 164 34 ILE CB C 38.78 . 1 119 164 34 ILE N N 120.4 . 1 120 165 35 GLU H H 8.394 . 1 121 165 35 GLU CA C 56.97 . 1 122 165 35 GLU CB C 30.34 . 1 123 165 35 GLU N N 124 . 1 124 166 36 GLU H H 8.374 . 1 125 166 36 GLU CA C 56.81 . 1 126 166 36 GLU CB C 30.3 . 1 127 166 36 GLU N N 122.3 . 1 128 167 37 LYS H H 8.352 . 1 129 167 37 LYS CA C 56.56 . 1 130 167 37 LYS CB C 33.05 . 1 131 167 37 LYS N N 122.2 . 1 132 168 38 SER H H 8.405 . 1 133 168 38 SER CA C 58.77 . 1 134 168 38 SER CB C 63.83 . 1 135 168 38 SER N N 116.6 . 1 136 169 39 GLY H H 8.529 . 1 137 169 39 GLY CA C 45.66 . 1 138 169 39 GLY N N 110.9 . 1 139 170 40 MET H H 8.263 . 1 140 170 40 MET CA C 55.82 . 1 141 170 40 MET CB C 32.86 . 1 142 170 40 MET N N 119.7 . 1 143 171 41 GLU H H 8.612 . 1 144 171 41 GLU CA C 57.46 . 1 145 171 41 GLU CB C 29.96 . 1 146 171 41 GLU N N 121.5 . 1 147 172 42 GLY H H 8.43 . 1 148 172 42 GLY CA C 45.58 . 1 149 172 42 GLY N N 109.6 . 1 150 173 43 ARG H H 8.054 . 1 151 173 43 ARG CA C 56.4 . 1 152 173 43 ARG CB C 30.79 . 1 153 173 43 ARG N N 120.5 . 1 154 174 44 LYS H H 8.285 . 1 155 174 44 LYS CA C 56.58 . 1 156 174 44 LYS CB C 33.23 . 1 157 174 44 LYS N N 122.3 . 1 158 175 45 LYS H H 8.303 . 1 159 175 45 LYS CA C 56.53 . 1 160 175 45 LYS CB C 33 . 1 161 175 45 LYS N N 122.4 . 1 162 176 46 MET H H 8.307 . 1 163 176 46 MET CA C 55.81 . 1 164 176 46 MET CB C 32.97 . 1 165 176 46 MET N N 121.3 . 1 166 177 47 PHE H H 8.195 . 1 167 177 47 PHE CA C 57.75 . 1 168 177 47 PHE CB C 39.65 . 1 169 177 47 PHE N N 120.5 . 1 170 178 48 GLU H H 8.344 . 1 171 178 48 GLU CA C 56.38 . 1 172 178 48 GLU CB C 30.67 . 1 173 178 48 GLU N N 122.6 . 1 174 179 49 ALA H H 8.338 . 1 175 179 49 ALA CA C 52.8 . 1 176 179 49 ALA CB C 19.33 . 1 177 179 49 ALA N N 125 . 1 178 180 50 GLY H H 8.365 . 1 179 180 50 GLY CA C 45.24 . 1 180 180 50 GLY N N 108.2 . 1 181 181 51 GLU H H 8.254 . 1 182 181 51 GLU CA C 56.47 . 1 183 181 51 GLU CB C 30.76 . 1 184 181 51 GLU N N 120.8 . 1 185 182 52 SER H H 8.023 . 1 186 182 52 SER CA C 60.02 . 1 187 182 52 SER CB C 64.96 . 1 188 182 52 SER N N 122.2 . 1 stop_ save_