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- PDB-6fwn: Structure and dynamics of the platelet integrin-binding C4 domain... -

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Basic information

Entry
Database: PDB / ID: 6fwn
TitleStructure and dynamics of the platelet integrin-binding C4 domain of von Willebrand factor
Componentsvon Willebrand factor
KeywordsBLOOD CLOTTING / von Willebrand Factor / vWC domain
Function / homology
Function and homology information


Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / Weibel-Palade body / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / Weibel-Palade body / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of intracellular signal transduction / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / blood coagulation / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / protein-folding chaperone binding / protease binding / : / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / Von Willebrand factor-like domain / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain ...von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / Von Willebrand factor-like domain / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot domain profile. / von Willebrand factor type C domain / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsXu, E.-R. / von Buelow, S. / Chen, P.-C. / Lenting, P.J. / Kolsek, K. / Aponte-Santamaria, C. / Simon, B. / Foot, J. / Obser, T. / Graeter, F. ...Xu, E.-R. / von Buelow, S. / Chen, P.-C. / Lenting, P.J. / Kolsek, K. / Aponte-Santamaria, C. / Simon, B. / Foot, J. / Obser, T. / Graeter, F. / Schneppenheim, R. / Denis, C.V. / Wilmanns, M. / Hennig, J.
CitationJournal: Blood / Year: 2019
Title: Structure and dynamics of the platelet integrin-binding C4 domain of von Willebrand factor.
Authors: Xu, E.R. / von Bulow, S. / Chen, P.C. / Lenting, P.J. / Kolsek, K. / Aponte-Santamaria, C. / Simon, B. / Foot, J. / Obser, T. / Schneppenheim, R. / Grater, F. / Denis, C.V. / Wilmanns, M. / Hennig, J.
History
DepositionMar 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: von Willebrand factor


Theoretical massNumber of molelcules
Total (without water)9,1221
Polymers9,1221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6680 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
Representative

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Components

#1: Protein von Willebrand factor / vWF


Mass: 9122.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first four residues in that sequence (GSMA) remain from the thrombin cleavage site and are not part of the native sequence.
Source: (gene. exp.) Homo sapiens (human) / Cell line: Extracellular / Gene: VWF, F8VWF / Organ: Blood / Plasmid: pHAT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04275
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic32D 1H-15N HSQC
123isotropic32D 1H-13C HSQC aliphatic
133isotropic32D 1H-13C HSQC aromatic
143isotropic32D 1H-13C HMQC
153isotropic33D HNCA
163isotropic33D HNCO
1113isotropic33D HN(CA)CB
1103isotropic33D CBCA(CO)NH
193isotropic33D HBHA(CO)NH
183isotropic33D H(CCO)NH
173isotropic33D C(CO)NH
1123isotropic33D (H)CCH-TOCSY
1153isotropic33D (H)CCH-TOCSY
1143isotropic33D 1H-15N NOESY-HSQC
1133isotropic33D 1H-13C NOESY-HSQC
1164isotropic33D 1H-13C HMQC-NOESY
1174isotropic33D 1H-13C HMQC-NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution3500 uM [U-13C; U-15N] von Willebrand Factor C4 domain, 20 mM sodium phosphate, 49.5 M H2O, 5.5 M D2O, 0.02 % w/v sodium azide, 90% H2O/10% D2O15N13C_sample90% H2O/10% D2O
solution4500 uM [U-13C; U-15N] von Willebrand Factor C4 domain, 20 mM sodium phosphate, 55 M D2O, 5 mM H2O, 0.02 % w/v sodium azide, 100% D2O15N13C_D2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMvon Willebrand Factor C4 domain[U-13C; U-15N]3
20 mMsodium phosphatenatural abundance3
49.5 MH2Onatural abundance3
5.5 MD2Onatural abundance3
0.02 % w/vsodium azidenatural abundance3
500 uMvon Willebrand Factor C4 domain[U-13C; U-15N]4
20 mMsodium phosphatenatural abundance4
55 MD2Onatural abundance4
5 mMH2Onatural abundance4
0.02 % w/vsodium azidenatural abundance4
Sample conditionsIonic strength: 0.04 M / Label: conditions_1 / pH: 6.5 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameClassification
ARIArefinement
CARAstructure solution
NMRPipestructure solution
TopSpinstructure solution
CYANAstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: WATER REFINEMENT
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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