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- PDB-2mhq: Solution structure of the major factor VIII binding region on von... -

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Basic information

Entry
Database: PDB / ID: 2mhq
TitleSolution structure of the major factor VIII binding region on von Willebrand factor
Componentsvon Willebrand factor
KeywordsBLOOD CLOTTING / von Willebrand factor / factor VIII / ensemble refinement
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 / positive regulation of intracellular signal transduction / 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 / 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 / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / protein-folding chaperone binding / protease binding / collagen-containing extracellular matrix / 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 / : / 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, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / : / 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 / 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 signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / 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 / torsion angle dynamics
Model detailsNot applicable, model1
AuthorsShiltagh, N. / Kirkpatrick, J. / Cabrita, L.D. / McKinnon, T.A.J. / Thalassinos, K. / Tuddenham, E.G.D. / Hansen, D.F.
CitationJournal: Blood / Year: 2014
Title: Solution structure of the major factor VIII binding region on von Willebrand factor.
Authors: Shiltagh, N. / Kirkpatrick, J. / Cabrita, L.D. / McKinnon, T.A. / Thalassinos, K. / Tuddenham, E.G. / Hansen, D.F.
History
DepositionDec 2, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Oct 30, 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
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: von Willebrand factor


Theoretical massNumber of molelcules
Total (without water)11,3511
Polymers11,3511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1not applicable

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Components

#1: Protein von Willebrand factor / vWF / von Willebrand antigen 2 / von Willebrand antigen II


Mass: 11351.278 Da / Num. of mol.: 1 / Fragment: Domains TIL' and E', UNP residues 766-864
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VWF, F8VWF / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): Shuffle / References: UniProt: P04275
Has protein modificationY
Sequence detailsQ91R (UNP RESIDUE 852) IS NATURAL VARIANT ACCORDING TO DATABASE P04275 (VWF_HUMAN), UNIPROTKB/SWISS-PROT.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D 15N HSQC-NOESY-15N HSQC
1613D HN(CACO)NH
1713D (H)CC(CO)NH
1813D H(CCCO)NH
1913D (H)CCH-TOCSY
11022D constant-time 1H-13C HSQC
11113D 1H-15N NOESY
11243D 1H-13C NOESY
1133{1H}15N steady-state NOE
114315N R1rho relaxation
115315N R1 relaxation
116515N R2-CPMG relaxation dispersion
117515N R2-CPMG relaxation dispersion
11862D IPAP-15N HSQC
11972D IPAP-15N HSQC
12082D IPAP-15N HSQC
12162D IPAP-E.COSY-15N HSQC
12282D IPAP-E.COSY-15N HSQC
12363D IPAP-HNCO(J-CA)
12483D IPAP-HNCO(J-CA)
12563D HN(CO)CA(J-CB)
12683D HN(CO)CA(J-CB)
12763D IPAP-(HA)CA(CO)NH
12883D IPAP-(HA)CA(CO)NH
12912D 1H-15N HSQC
13012D 1H-13C HSQC
13112D constant-time 1H-13C HSQC
13242D 1H-13C HSQC
13342D constant-time 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
1300 mM [U-13C; U-15N] VWF TIL'E'-1, 20 mM sodium phosphate-2, 100 mM sodium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
2300 mM [U-10% 13C] VWF TIL'E'-4, 20 mM sodium phosphate-5, 100 mM sodium chloride-6, 90% H2O/10% D2O90% H2O/10% D2O
3300 mM [U-15N] VWF TIL'E'-7, 20 mM sodium phosphate-8, 100 mM sodium chloride-9, 90% H2O/10% D2O90% H2O/10% D2O
4300 mM [U-13C; U-15N] VWF TIL'E'-10, 20 mM sodium phosphate-11, 100 mM sodium chloride-12, 90% H2O/10% D2O90% H2O/10% D2O
5300 mM [U-15N] VWF TIL'E'-13, 20 mM sodium phosphate-14, 100 mM sodium chloride-15, 90% H2O/10% D2O90% H2O/10% D2O
6300 mM [U-13C; U-15N] VWF TIL'E'-16, 20 mM sodium phosphate-17, 100 mM sodium chloride-18, 90% H2O/10% D2O90% H2O/10% D2O
7300 mM [U-13C; U-15N] VWF TIL'E'-19, 20 mM sodium phosphate-20, 100 mM sodium chloride-21, 5 mg/mL Pf1 phage-22, 90% H2O/10% D2O90% H2O/10% D2O
8300 mM [U-13C; U-15N] VWF TIL'E'-23, 20 mM sodium phosphate-24, 100 mM sodium chloride-25, 2 % w/v pentaethylene glycol dodecyl ether-26, 50 mM n-hexanol-27, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 mMVWF TIL'E'-1[U-13C; U-15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
300 mMVWF TIL'E'-4[U-10% 13C]2
20 mMsodium phosphate-52
100 mMsodium chloride-62
300 mMVWF TIL'E'-7[U-15N]3
20 mMsodium phosphate-83
100 mMsodium chloride-93
300 mMVWF TIL'E'-10[U-13C; U-15N]4
20 mMsodium phosphate-114
100 mMsodium chloride-124
300 mMVWF TIL'E'-13[U-15N]5
20 mMsodium phosphate-145
100 mMsodium chloride-155
300 mMVWF TIL'E'-16[U-13C; U-15N]6
20 mMsodium phosphate-176
100 mMsodium chloride-186
300 mMVWF TIL'E'-19[U-13C; U-15N]7
20 mMsodium phosphate-207
100 mMsodium chloride-217
5 mg/mLPf1 phage-227
300 mMVWF TIL'E'-23[U-13C; U-15N]8
20 mMsodium phosphate-248
100 mMsodium chloride-258
2 %pentaethylene glycol dodecyl ether-268
50 mMn-hexanol-278
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker Avance IIIBrukerAVANCE III5002
Bruker Avance IIIBrukerAVANCE III7003

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.2DVariancollection
TopSpin2.1Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
Xplor-NIHrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Ensemble of 10 replicas was calculated collectively using ensemble-averaged approach (ensemble-refinement).
NMR representativeSelection criteria: not applicable
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10 / Representative conformer: 1

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