data_25597 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of Dynorphin 1-13 bound to Kappa Opioid Receptor ; _BMRB_accession_number 25597 _BMRB_flat_file_name bmr25597.str _Entry_type original _Submission_date 2015-05-06 _Accession_date 2015-05-06 _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 O'Connor Casey . . 2 White Kate . . 3 Doncescu Nathalie . . 4 Didenko Tatiana . . 5 Roth Bryan L. . 6 Czaplicki Georges . . 7 Stevens Raymond C. . 8 Wuthrich Kurt . . 9 Milon Alain . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 109 "13C chemical shifts" 18 "15N chemical shifts" 18 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-08-24 update BMRB 'update entry citation' 2015-09-10 original author 'original release' stop_ _Original_release_date 2015-09-10 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR structure and dynamics of the agonist dynorphin peptide bound to the human kappa opioid receptor ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26372966 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 O'Connor Casey . . 2 White Kate . . 3 Doncescu Nathalie . . 4 Didenko Tatiana . . 5 Roth Bryan L. . 6 Czaplicki Georges . . 7 Stevens Raymond C. . 8 Wuthrich Kurt . . 9 Milon Alain . . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_volume 112 _Journal_issue 38 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11852 _Page_last 11857 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Dynorphin 1-13 bound to Kappa Opioid Receptor' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity $Dynorphin_1-13 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_Dynorphin_1-13 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Dynorphin_1-13 _Molecular_mass 1609.012 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence ; YGGFLRRIRPKLK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 TYR 2 2 GLY 3 3 GLY 4 4 PHE 5 5 LEU 6 6 ARG 7 7 ARG 8 8 ILE 9 9 ARG 10 10 PRO 11 11 LYS 12 12 LEU 13 13 LYS 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 $Dynorphin_1-13 Human 9606 Eukaryota Metazoa Homo sapiens 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 _Details $Dynorphin_1-13 'chemical synthesis' . . . . . 'SYNTHESIS OF THE PEPTIDE WAS PERFORMED BY A SOLID PHASE METHOD USING FMOC CHEMISTRY.' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelle _Details ; After data acquisition in the presence of KOR, the agonist JDTic was added to a final concentration of 1mM and the complete set of NMR experiments was performed on the same sample under identical conditions, in order to obtain information on the non-specific binding of dynorphin. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Dynorphin_1-13 1 mM [U-15N-GFLI] 'potassium chloride' 150 mM 'natural abundance' MES 40 mM [U-2H] DSS 100 uM 'natural abundance' KOR 10 uM 'natural abundance' DDM 8 mM 'natural abundance' CHS 1.6 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type micelle _Details ; After data acquisition in the presence of KOR, the agonist JDTic was added to a final concentration of 1mM and the complete set of NMR experiments was performed on the same sample under identical conditions, in order to obtain information on the non-specific binding of dynorphin. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Dynorphin_1-13 1 mM '[U-15N-GFLIR; U-13C-R]' 'potassium chloride' 150 mM 'natural abundance' MES 40 mM [U-2H] DSS 100 uM 'natural abundance' KOR 10 uM 'natural abundance' DDM 8 mM 'natural abundance' CHS 1.6 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 3.2 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' processing stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 14 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'geometry optimization' 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance III' _Field_strength 800 _Details 'TCI 5mm cryoprobe' save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details 'TXI 5mm probe' save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance III' _Field_strength 700 _Details 'TXI 1.7mm probe' save_ save_spectrometer_4 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance III' _Field_strength 600 _Details 'TCI 5mm cryoprobe' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_2D_HNCACB_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HNCACB' _Sample_label $sample_2 save_ save_15N_T1_T2_hetNOE_6 _Saveframe_category NMR_applied_experiment _Experiment_name '15N T1 T2 hetNOE' _Sample_label $sample_1 save_ save_15N_T2_7 _Saveframe_category NMR_applied_experiment _Experiment_name '15N T2' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.1 . pH pressure 1 . atm temperature 280 . 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 internal direct . . . 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $TOPSPIN stop_ loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-15N HSQC' '2D 1H-13C HSQC' '2D HNCACB' 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 entity _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 1 1 TYR HA H 4.239 0.007 1 2 1 1 TYR HB2 H 3.134 0.007 1 3 1 1 TYR HB3 H 3.134 0.007 1 4 1 1 TYR HD1 H 7.167 0.007 1 5 1 1 TYR HD2 H 7.167 0.007 1 6 1 1 TYR HE1 H 6.870 0.007 1 7 1 1 TYR HE2 H 6.870 0.007 1 8 2 2 GLY H H 8.690 0.007 1 9 2 2 GLY HA2 H 3.906 0.007 1 10 2 2 GLY HA3 H 3.906 0.007 1 11 2 2 GLY N N 111.189 0.07 1 12 3 3 GLY H H 8.038 0.007 1 13 3 3 GLY HA2 H 3.864 0.007 1 14 3 3 GLY HA3 H 3.864 0.007 1 15 3 3 GLY N N 107.332 0.07 1 16 4 4 PHE H H 8.202 0.007 1 17 4 4 PHE HA H 4.591 0.007 1 18 4 4 PHE HB2 H 3.019 0.007 2 19 4 4 PHE HB3 H 3.104 0.007 2 20 4 4 PHE HD1 H 7.240 0.007 1 21 4 4 PHE HD2 H 7.240 0.007 1 22 4 4 PHE HE1 H 7.353 0.007 1 23 4 4 PHE HE2 H 7.353 0.007 1 24 4 4 PHE HZ H 7.307 0.007 1 25 4 4 PHE N N 118.585 0.07 1 26 5 5 LEU H H 8.279 0.007 1 27 5 5 LEU HA H 4.292 0.007 1 28 5 5 LEU HB2 H 1.579 0.007 1 29 5 5 LEU HB3 H 1.579 0.007 1 30 5 5 LEU HG H 1.508 0.007 1 31 5 5 LEU HD1 H 0.841 0.007 2 32 5 5 LEU HD2 H 0.895 0.007 2 33 5 5 LEU N N 123.075 0.07 1 34 6 6 ARG H H 8.312 0.007 1 35 6 6 ARG HA H 4.260 0.007 1 36 6 6 ARG HB2 H 1.749 0.007 2 37 6 6 ARG HB3 H 1.814 0.007 2 38 6 6 ARG HG2 H 1.589 0.007 2 39 6 6 ARG HG3 H 1.642 0.007 2 40 6 6 ARG HD2 H 3.197 0.007 1 41 6 6 ARG HD3 H 3.197 0.007 1 42 6 6 ARG HE H 7.242 0.007 1 43 6 6 ARG HH11 H 6.911 0.007 1 44 6 6 ARG HH12 H 6.911 0.007 1 45 6 6 ARG HH21 H 6.507 0.007 1 46 6 6 ARG HH22 H 6.507 0.007 1 47 6 6 ARG C C 176.067 0.10 1 48 6 6 ARG CA C 55.970 0.10 1 49 6 6 ARG CB C 30.595 0.10 1 50 6 6 ARG CG C 27.094 0.10 1 51 6 6 ARG CD C 43.339 0.10 1 52 6 6 ARG CZ C 159.447 0.10 1 53 6 6 ARG N N 121.173 0.07 1 54 6 6 ARG NE N 84.48 0.07 1 55 6 6 ARG NH1 N 71.99 0.07 2 56 6 6 ARG NH2 N 71.05 0.07 2 57 7 7 ARG H H 8.396 0.007 1 58 7 7 ARG HA H 4.312 0.007 1 59 7 7 ARG HB2 H 1.748 0.007 2 60 7 7 ARG HB3 H 1.805 0.007 2 61 7 7 ARG HG2 H 1.565 0.007 2 62 7 7 ARG HG3 H 1.619 0.007 2 63 7 7 ARG HD2 H 3.174 0.007 1 64 7 7 ARG HD3 H 3.174 0.007 1 65 7 7 ARG HE H 7.242 0.007 1 66 7 7 ARG HH11 H 6.507 0.007 1 67 7 7 ARG HH12 H 6.507 0.007 1 68 7 7 ARG HH21 H 6.911 0.007 1 69 7 7 ARG HH22 H 6.911 0.007 1 70 7 7 ARG C C 176.067 0.10 1 71 7 7 ARG CA C 55.970 0.10 1 72 7 7 ARG CB C 30.783 0.10 1 73 7 7 ARG CG C 27.094 0.10 1 74 7 7 ARG CD C 43.339 0.10 1 75 7 7 ARG CZ C 159.447 0.10 1 76 7 7 ARG N N 121.712 0.07 1 77 7 7 ARG NE N 84.48 0.07 1 78 7 7 ARG NH1 N 71.05 0.07 2 79 7 7 ARG NH2 N 71.99 0.07 2 80 8 8 ILE H H 8.374 0.007 1 81 8 8 ILE HA H 4.143 0.007 1 82 8 8 ILE HB H 1.829 0.007 1 83 8 8 ILE HG12 H 1.465 0.007 2 84 8 8 ILE HG13 H 1.179 0.007 2 85 8 8 ILE HG2 H 0.872 0.007 1 86 8 8 ILE HD1 H 0.841 0.007 1 87 8 8 ILE N N 122.082 0.07 1 88 9 9 ARG H H 8.569 0.007 1 89 9 9 ARG HA H 4.606 0.007 1 90 9 9 ARG HB2 H 1.735 0.007 2 91 9 9 ARG HB3 H 1.851 0.007 2 92 9 9 ARG HG3 H 1.663 0.007 1 93 9 9 ARG HD2 H 3.209 0.007 1 94 9 9 ARG HD3 H 3.209 0.007 1 95 9 9 ARG HE H 7.242 0.007 1 96 9 9 ARG HH11 H 6.507 0.007 1 97 9 9 ARG HH12 H 6.507 0.007 1 98 9 9 ARG HH21 H 6.911 0.007 1 99 9 9 ARG HH22 H 6.911 0.007 1 100 9 9 ARG C C 174.005 0.10 1 101 9 9 ARG CA C 53.858 0.10 1 102 9 9 ARG CB C 30.116 0.10 1 103 9 9 ARG CG C 27.094 0.10 1 104 9 9 ARG CD C 43.339 0.10 1 105 9 9 ARG CZ C 159.447 0.10 1 106 9 9 ARG N N 126.054 0.07 1 107 9 9 ARG NE N 84.48 0.07 1 108 9 9 ARG NH1 N 71.05 0.07 2 109 9 9 ARG NH2 N 71.99 0.07 2 110 10 10 PRO HA H 4.398 0.007 1 111 10 10 PRO HB2 H 1.856 0.007 2 112 10 10 PRO HB3 H 2.294 0.007 2 113 10 10 PRO HG2 H 2.004 0.007 2 114 10 10 PRO HG3 H 1.730 0.007 2 115 10 10 PRO HD2 H 3.829 0.007 2 116 10 10 PRO HD3 H 3.650 0.007 2 117 11 11 LYS H H 8.520 0.007 1 118 11 11 LYS HA H 4.284 0.007 1 119 11 11 LYS HB2 H 1.753 0.007 2 120 11 11 LYS HB3 H 1.821 0.007 2 121 11 11 LYS HG2 H 1.433 0.007 2 122 11 11 LYS HG3 H 1.474 0.007 2 123 11 11 LYS HD2 H 1.695 0.007 1 124 11 11 LYS HD3 H 1.695 0.007 1 125 11 11 LYS HE2 H 3.009 0.007 1 126 11 11 LYS HE3 H 3.009 0.007 1 127 11 11 LYS HZ H 7.580 0.007 1 128 12 12 LEU H H 8.481 0.007 1 129 12 12 LEU HA H 4.341 0.007 1 130 12 12 LEU HB2 H 1.605 0.007 1 131 12 12 LEU HB3 H 1.605 0.007 1 132 12 12 LEU HG H 1.656 0.007 1 133 12 12 LEU HD1 H 0.868 0.007 2 134 12 12 LEU HD2 H 0.932 0.007 2 135 12 12 LEU N N 123.681 0.07 1 136 13 13 LYS H H 7.938 0.007 1 137 13 13 LYS HA H 4.126 0.007 1 138 13 13 LYS HB2 H 1.717 0.007 2 139 13 13 LYS HB3 H 1.796 0.007 2 140 13 13 LYS HG2 H 1.376 0.007 1 141 13 13 LYS HD2 H 1.673 0.007 1 142 13 13 LYS HD3 H 1.673 0.007 1 143 13 13 LYS HE2 H 2.991 0.007 1 144 13 13 LYS HE3 H 2.991 0.007 1 145 13 13 LYS HZ H 7.580 0.007 1 stop_ save_