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- PDB-6f3x: Backbone structure of Des-Arg10-Kallidin (DAKD) peptide in frozen... -

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Basic information

Entry
Database: PDB / ID: 6f3x
TitleBackbone structure of Des-Arg10-Kallidin (DAKD) peptide in frozen DDM/CHS detergent micelle solution 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
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

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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 area1300 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the least restraint violations
RepresentativeModel #9closest 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
163isotropic12D 15N-13C TEDOR
174isotropic12D 13C-13C DQ-SQ
184isotropic12D 15N-13C TEDOR
195isotropic12D 13C-13C DQ-SQ
1105isotropic12D 15N-13C TEDOR
1116isotropic12D 13C-13C DQ-SQ
1126isotropic12D 15N-13C TEDOR

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid1300 uM [U-13C; U-15N] K1 Des-Arg10-Kallidin (DAKD), 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 DAKD in DDM/CHS detergent micelleUCN-K1 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
solid2300 uM [U-13C; U-15N] R2S7 Des-Arg10-Kallidin (DAKD), 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 DAKD in DDM/CHS detergent micelleUCN-R2S7 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
solid3300 uM [U-13C; U-15N] P3 Des-Arg10-Kallidin (DAKD), 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 DAKD in DDM/CHS detergent micelleUCN-P3 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
solid4300 uM [U-13C; U-15N] P4 Des-Arg10-Kallidin (DAKD), 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 DAKD in DDM/CHS detergent micelleUCN-P4 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
solid5300 uM [U-13C; U-15N] G5F6 Des-Arg10-Kallidin (DAKD), 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 DAKD in DDM/CHS detergent micelleUCN-G5F6 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
solid6300 uM [U-13C; U-15N] S7P9 Des-Arg10-Kallidin (DAKD), 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 DAKD in DDM/CHS detergent micelleUCN-S7P9 DAKD10% H2O/ 40%D2O/ 50% d8-glycerol
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] K11
10 mMAMUPOLnot labeled1
50 mMHEPESnot labeled1
150 mMNaClnot labeled1
4 % w/vDDMnot labeled1
0.4 % w/vCHSnot labeled1
300 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] R2S72
10 mMAMUPOLnot labeled2
50 mMHEPESnot labeled2
150 mMNaClnot labeled2
4 % w/vDDMnot labeled2
0.4 % w/vCHSnot labeled2
300 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] P33
10 mMAMUPOLnot labeled3
50 mMHEPESnot labeled3
150 mMNaClnot labeled3
4 % w/vDDMnot labeled3
0.4 % w/vCHSnot labeled3
300 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] P44
10 mMAMUPOLnot labeled4
50 mMHEPESnot labeled4
150 mMNaClnot labeled4
4 % w/vDDMnot labeled4
0.4 % w/vCHSnot labeled4
300 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] G5F65
10 mMAMUPOLnot labeled5
50 mMHEPESnot labeled5
150 mMNaClnot labeled5
4 % w/vDDMnot labeled5
0.4 % w/vCHSnot labeled5
300 uMDes-Arg10-Kallidin (DAKD)[U-13C; U-15N] S7P96
10 mMAMUPOLnot labeled6
50 mMHEPESnot labeled6
150 mMNaClnot labeled6
4 % w/vDDMnot labeled6
0.4 % w/vCHSnot labeled6
Sample conditionsIonic 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 Biospinprocessing
TALOS+Shen, Delaglio, Cornilescu, Baxdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 2
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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