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- PDB-6f3y: Backbone structure of Des-Arg10-Kallidin (DAKD) peptide bound to ... -

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Basic information

Entry
Database: PDB / ID: 6f3y
TitleBackbone structure of Des-Arg10-Kallidin (DAKD) peptide bound to human Bradykinin 1 Receptor (B1R) determined by DNP-enhanced MAS SSNMR
ComponentsKininogen-1
KeywordsMEMBRANE PROTEIN / GPCR / DNP
Function / homology
Function and homology information


negative regulation of cell adhesion / negative regulation of blood coagulation / cysteine-type endopeptidase inhibitor activity / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen / negative regulation of proteolysis / Post-translational protein phosphorylation / hormone activity / vasodilation ...negative regulation of cell adhesion / negative regulation of blood coagulation / cysteine-type endopeptidase inhibitor activity / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen / negative regulation of proteolysis / Post-translational protein phosphorylation / hormone activity / vasodilation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / heparin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / inflammatory response / positive regulation of apoptotic process / endoplasmic reticulum lumen / signaling receptor binding / extracellular space / extracellular exosome / zinc ion binding / extracellular region / plasma membrane
Similarity search - Function
HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / : / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / torsion angle dynamics / na
AuthorsMao, J. / Kuenze, G. / Joedicke, L. / Meiler, J. / Michel, H. / Glaubitz, C.
Funding support Germany, United States, 4items
OrganizationGrant numberCountry
German Research FoundationSFB 807 Germany
German Research FoundationCluster of Excellence Frankfurt Macromolecular Complexes Germany
German Research FoundationGL 307/8-1 Germany
National Institutes of HealthR01 GM080403, R01 GM099842, R01 GM073151 United States
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: The molecular basis of subtype selectivity of human kinin G-protein-coupled receptors.
Authors: Joedicke, L. / Mao, J. / Kuenze, G. / Reinhart, C. / Kalavacherla, T. / Jonker, H.R.A. / Richter, C. / Schwalbe, H. / Meiler, J. / Preu, J. / Michel, H. / Glaubitz, C.
History
DepositionNov 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Aug 21, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.6Jun 23, 2021Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.field_strength
Revision 1.7Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.8Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kininogen-1


Theoretical massNumber of molelcules
Total (without water)1,0341
Polymers1,0341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1320 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the least restraint violations
RepresentativeModel #4closest to the average

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Components

#1: Protein/peptide Kininogen-1 / Alpha-2-thiol proteinase inhibitor / Fitzgerald factor / High molecular weight kininogen / HMWK / ...Alpha-2-thiol proteinase inhibitor / Fitzgerald factor / High molecular weight kininogen / HMWK / Williams-Fitzgerald-Flaujeac factor


Mass: 1034.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P01042

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 13C-13C DQ-SQ
121isotropic12D 15N-13C TEDOR
132isotropic12D 13C-13C DQ-SQ
142isotropic12D 15N-13C TEDOR
153isotropic12D 13C-13C DQ-SQ
193isotropic12D 15N-13C TEDOR
184isotropic12D 13C-13C DQ-SQ
174isotropic12D 15N-13C TEDOR
165isotropic12D 13C-13C DQ-SQ
1105isotropic12D 15N-13C TEDOR
1116isotropic12D 13C-13C DQ-SQ
1136isotropic12D 13C-13C DQ-SQ
1126isotropic11D REDOR/DQF double-filter 13C

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid1312.5 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-glycerolfrozen solution of B1R-DAKD complex in DDM/CHS detergent micelleUCN-K1 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
solid2312.5 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-glycerolfrozen solution of B1R-DAKD complex in DDM/CHS detergent micelleUCN-R2S7 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
solid3312.5 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-glycerolfrozen solution of B1R-DAKD complex in DDM/CHS detergent micelleUCN-P3 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
solid4312.5 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-glycerolfrozen solution of B1R-DAKD complex in DDM/CHS detergent micelleUCN-P4 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
solid5312.5 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-glycerolfrozen solution of B1R-DAKD complex in DDM/CHS detergent micelleUCN-G5F6 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
solid6312.5 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-glycerolfrozen solution of B1R-DAKD complex in DDM/CHS detergent micelleUCN-S7P9 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
312.5 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] K11
312.5 uMhuman B1Rnot labeled1
10 mMAMUPOLnot labeled1
50 mMHEPESnot labeled1
150 mMNaClnot labeled1
4 % w/vDDMnot labeled1
0.4 % w/vCHSnot labeled1
312.5 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] R2S72
312.5 uMhuman B1Rnot labeled2
10 mMAMUPOLnot labeled2
50 mMHEPESnot labeled2
150 mMNaClnot labeled2
4 % w/vDDMnot labeled2
0.4 % w/vCHSnot labeled2
312.5 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] P33
312.5 uMhuman B1Rnot labeled3
10 mMAMUPOLnot labeled3
50 mMHEPESnot labeled3
150 mMNaClnot labeled3
4 % w/vDDMnot labeled3
0.4 % w/vCHSnot labeled3
312.5 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] P44
312.5 uMhuman B1Rnot labeled4
10 mMAMUPOLnot labeled4
50 mMHEPESnot labeled4
150 mMNaClnot labeled4
4 % w/vDDMnot labeled4
0.4 % w/vCHSnot labeled4
312.5 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] G5F65
312.5 uMhuman B1Rnot labeled5
10 mMAMUPOLnot labeled5
50 mMHEPESnot labeled5
150 mMNaClnot labeled5
4 % w/vDDMnot labeled5
0.4 % w/vCHSnot labeled5
312.5 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] S7P96
312.5 uMhuman B1Rnot labeled6
10 mMAMUPOLnot labeled6
50 mMHEPESnot labeled6
150 mMNaClnot labeled6
4 % w/vDDMnot labeled6
0.4 % w/vCHSnot labeled6
Sample conditionsDetails: frozen solution of B1R-DAKD complex in DDM/CHS detergent micelle
Ionic strength: 175 mM / Label: DNP / pH: 7.6 / Pressure: 1 atm / Temperature: 110 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 400 MHz / Details: SSNMR spectrometer

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospinchemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
TALOS-NShen, Baxrefinement
PREDITORBerjanskii, Neal, Wishartrefinement
Flexible-meccanoOzone, Bauer, Salmon, Huang, Jensen, Segard, Bernado, Charavay, Blackledgerefinement
SHIFTX1.1Neal, Nip, Zhang, Wishartrefinement
Circos0.69.3Krzywinski, Schein, Birol, Connors, Gascoyne, Horsman, Jones, A Marrarefinement
TALOS+Shen, Delaglio, Cornilescu, Baxdata analysis
Refinement
MethodSoftware ordinalDetails
torsion angle dynamics1
na7used in joint analysis, see paper for more details
na8used in joint analysis, see paper for more details
na9used in joint analysis, see paper for more details
na10used in joint analysis, see paper for more details
na11used in joint analysis, see paper for more details
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 500 / Conformers submitted total number: 10

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