data_34209 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Backbone structure of Des-Arg10-Kallidin (DAKD) peptide bound to human Bradykinin 1 Receptor (B1R) determined by DNP-enhanced MAS SSNMR ; _BMRB_accession_number 34209 _BMRB_flat_file_name bmr34209.str _Entry_type original _Submission_date 2017-11-29 _Accession_date 2017-11-29 _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 Mao J. . . 2 Kuenze G. . . 3 Joedicke L. . . 4 Meiler J. . . 5 Michel H. . . 6 Glaubitz C. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 25 "15N chemical shifts" 8 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-02-21 update BMRB 'update entry citation' 2018-01-05 original author 'original release' stop_ _Original_release_date 2018-01-03 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; The molecular basis of subtype selectivity of human kinin G-protein-coupled receptors. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29334381 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Joedicke Lisa . . 2 Mao Jiafei . . 3 Kuenze Georg . . 4 Reinhart Christoph . . 5 Kalavacherla Tejaswi . . 6 Jonker Hendrik . . 7 Richter Christian . . 8 Schwalbe Harald . . 9 Meiler Jens . . 10 Preu Julia . . 11 Michel Hartmut . . 12 Glaubitz Clemens . . stop_ _Journal_abbreviation 'Nat. Chem. Biol.' _Journal_name_full 'Nature chemical biology' _Journal_volume 14 _Journal_issue 3 _Journal_ISSN 1552-4469 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 284 _Page_last 290 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Kininogen-1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _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 entity_1 _Molecular_mass 1034.210 _Mol_thiol_state 'not present' _Details ; DAKD peptide bound to human B1R Synonyms: Lys-des-Arg9 Bradykinin ; ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence ; KRPPGFSPF ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 ARG 3 PRO 4 PRO 5 GLY 6 PHE 7 SER 8 PRO 9 PHE 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 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 $entity_1 'chemical synthesis' . . . . . 'This sequence occurs naturally in humans' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solid _Details ; 312.5 uM [U-13C; U-15N] K1 Des-Arg10-Kallidin (DAKD), 312.5 uM not labeled human B1R, 10 mM not labeled AMUPOL, 50 mM not labeled HEPES, 150 mM not labeled NaCl, 4 % w/v not labeled DDM, 0.4 % w/v not labeled CHS, 10% H2O/ 40%D2O/ 50% d8-glycerol ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 312.5 uM '[U-13C; U-15N] K1' 'human B1R' 312.5 uM 'natural abundance' AMUPOL 10 mM 'natural abundance' HEPES 50 mM 'natural abundance' NaCl 150 mM 'natural abundance' DDM 4 '% w/v' 'natural abundance' CHS 0.4 '% w/v' 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solid _Details ; 312.5 uM [U-13C; U-15N] R2S7 Des-Arg10-Kallidin (DAKD), 312.5 uM not labeled human B1R, 10 mM not labeled AMUPOL, 50 mM not labeled HEPES, 150 mM not labeled NaCl, 4 % w/v not labeled DDM, 0.4 % w/v not labeled CHS, 10% H2O/ 40%D2O/ 50% d8-glycerol ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 312.5 uM '[U-13C; U-15N] R2S7' 'human B1R' 312.5 uM 'natural abundance' AMUPOL 10 mM 'natural abundance' HEPES 50 mM 'natural abundance' NaCl 150 mM 'natural abundance' DDM 4 '% w/v' 'natural abundance' CHS 0.4 '% w/v' 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solid _Details ; 312.5 uM [U-13C; U-15N] P3 Des-Arg10-Kallidin (DAKD), 312.5 uM not labeled human B1R, 10 mM not labeled AMUPOL, 50 mM not labeled HEPES, 150 mM not labeled NaCl, 4 % w/v not labeled DDM, 0.4 % w/v not labeled CHS, 10% H2O/ 40%D2O/ 50% d8-glycerol ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 312.5 uM '[U-13C; U-15N] P3' 'human B1R' 312.5 uM 'natural abundance' AMUPOL 10 mM 'natural abundance' HEPES 50 mM 'natural abundance' NaCl 150 mM 'natural abundance' DDM 4 '% w/v' 'natural abundance' CHS 0.4 '% w/v' 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solid _Details ; 312.5 uM [U-13C; U-15N] P4 Des-Arg10-Kallidin (DAKD), 312.5 uM not labeled human B1R, 10 mM not labeled AMUPOL, 50 mM not labeled HEPES, 150 mM not labeled NaCl, 4 % w/v not labeled DDM, 0.4 % w/v not labeled CHS, 10% H2O/ 40%D2O/ 50% d8-glycerol ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 312.5 uM '[U-13C; U-15N] P4' 'human B1R' 312.5 uM 'natural abundance' AMUPOL 10 mM 'natural abundance' HEPES 50 mM 'natural abundance' NaCl 150 mM 'natural abundance' DDM 4 '% w/v' 'natural abundance' CHS 0.4 '% w/v' 'natural abundance' stop_ save_ save_sample_5 _Saveframe_category sample _Sample_type solid _Details ; 312.5 uM [U-13C; U-15N] G5F6 Des-Arg10-Kallidin (DAKD), 312.5 uM not labeled human B1R, 10 mM not labeled AMUPOL, 50 mM not labeled HEPES, 150 mM not labeled NaCl, 4 % w/v not labeled DDM, 0.4 % w/v not labeled CHS, 10% H2O/ 40%D2O/ 50% d8-glycerol ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 312.5 uM '[U-13C; U-15N] G5F6' 'human B1R' 312.5 uM 'natural abundance' AMUPOL 10 mM 'natural abundance' HEPES 50 mM 'natural abundance' NaCl 150 mM 'natural abundance' DDM 4 '% w/v' 'natural abundance' CHS 0.4 '% w/v' 'natural abundance' stop_ save_ save_sample_6 _Saveframe_category sample _Sample_type solid _Details ; 312.5 uM [U-13C; U-15N] S7P9 Des-Arg10-Kallidin (DAKD), 312.5 uM not labeled human B1R, 10 mM not labeled AMUPOL, 50 mM not labeled HEPES, 150 mM not labeled NaCl, 4 % w/v not labeled DDM, 0.4 % w/v not labeled CHS, 10% H2O/ 40%D2O/ 50% d8-glycerol ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 312.5 uM '[U-13C; U-15N] S7P9' 'human B1R' 312.5 uM 'natural abundance' AMUPOL 10 mM 'natural abundance' HEPES 50 mM 'natural abundance' NaCl 150 mM 'natural abundance' DDM 4 '% w/v' 'natural abundance' CHS 0.4 '% w/v' 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'chemical shift assignment' collection 'data analysis' processing stop_ _Details . save_ save_software_3 _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_4 _Saveframe_category software _Name TALOS-N _Version . loop_ _Vendor _Address _Electronic_address 'Shen, Bax' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_5 _Saveframe_category software _Name PREDITOR _Version . loop_ _Vendor _Address _Electronic_address 'Berjanskii, Neal, Wishart' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_6 _Saveframe_category software _Name flexible-meccano _Version . loop_ _Vendor _Address _Electronic_address 'Ozone, Bauer, Salmon, Huang, Jensen, Segard, Bernado, Charavay, Blackledge' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_7 _Saveframe_category software _Name SHIFTX _Version 1.1 loop_ _Vendor _Address _Electronic_address 'Neal, Nip, Zhang, Wishart' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_8 _Saveframe_category software _Name CIRCOS _Version 0.69.3 loop_ _Vendor _Address _Electronic_address 'Krzywinski, Schein, Birol, Connors, Gascoyne, Horsman, Jones, A Marra' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_9 _Saveframe_category software _Name TALOS+ _Version . loop_ _Vendor _Address _Electronic_address 'Shen, Delaglio, Cornilescu, Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceII _Field_strength 400.197 _Details 'SSNMR spectrometer' save_ ############################# # NMR applied experiments # ############################# save_2D_13C-13C_DQ-SQ_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DQ-SQ' _Sample_label $sample_1 save_ save_2D_15N-13C_TEDOR_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C TEDOR' _Sample_label $sample_1 save_ save_2D_13C-13C_DQ-SQ_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DQ-SQ' _Sample_label $sample_2 save_ save_2D_15N-13C_TEDOR_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C TEDOR' _Sample_label $sample_2 save_ save_2D_13C-13C_DQ-SQ_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DQ-SQ' _Sample_label $sample_3 save_ save_2D_13C-13C_DQ-SQ_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DQ-SQ' _Sample_label $sample_5 save_ save_2D_15N-13C_TEDOR_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C TEDOR' _Sample_label $sample_4 save_ save_2D_13C-13C_DQ-SQ_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DQ-SQ' _Sample_label $sample_4 save_ save_2D_15N-13C_TEDOR_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C TEDOR' _Sample_label $sample_3 save_ save_2D_15N-13C_TEDOR_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C TEDOR' _Sample_label $sample_5 save_ save_2D_13C-13C_DQ-SQ_11 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DQ-SQ' _Sample_label $sample_6 save_ save_1D_REDOR/DQF_double-filter_13C_12 _Saveframe_category NMR_applied_experiment _Experiment_name '1D REDOR/DQF double-filter 13C' _Sample_label $sample_6 save_ save_2D_13C-13C_DQ-SQ_13 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DQ-SQ' _Sample_label $sample_6 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' 175 . mM pH 7.6 . pH pressure 1 . atm temperature 110 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 TSP C 13 'methyl carbons' ppm 0 na direct . . . 1 'liquid anhydrous ammonia' N 15 nitrogen ppm 0 na indirect . . . 0.402979940 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 13C-13C DQ-SQ' '2D 15N-13C TEDOR' '1D REDOR/DQF double-filter 13C' stop_ loop_ _Sample_label $sample_1 $sample_2 $sample_3 $sample_5 $sample_4 $sample_6 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _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 LYS C C 173.800 . 1 2 1 1 LYS CA C 55.900 . 1 3 1 1 LYS CB C 33.400 . 1 4 2 2 ARG C C 174.800 . 1 5 2 2 ARG CA C 55.000 . 1 6 2 2 ARG CB C 30.800 . 1 7 2 2 ARG N N 121.500 . 1 8 3 3 PRO C C 175.700 . 1 9 3 3 PRO CA C 61.700 . 1 10 3 3 PRO CB C 31.200 . 1 11 3 3 PRO N N 133.900 . 1 12 4 4 PRO C C 177.400 . 1 13 4 4 PRO CA C 63.500 . 1 14 4 4 PRO CB C 32.500 . 1 15 4 4 PRO N N 131.700 . 1 16 5 5 GLY C C 174.700 . 1 17 5 5 GLY CA C 45.200 . 1 18 5 5 GLY N N 111.900 . 1 19 6 6 PHE C C 178.500 . 1 20 6 6 PHE CA C 59.000 . 1 21 6 6 PHE CB C 40.100 . 1 22 6 6 PHE N N 118.700 . 1 23 7 7 SER C C 174.400 . 1 24 7 7 SER CA C 55.400 . 1 25 7 7 SER CB C 62.600 . 1 26 7 7 SER N N 121.800 . 1 27 8 8 PRO C C 175.900 . 1 28 8 8 PRO CA C 62.700 . 1 29 8 8 PRO CB C 32.700 . 1 30 8 8 PRO N N 135.100 . 1 31 9 9 PHE CA C 57.300 . 1 32 9 9 PHE CB C 39.400 . 1 33 9 9 PHE N N 124.400 . 1 stop_ save_