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- PDB-5bv8: G1324S mutation in von Willebrand Factor A1 domain -

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Basic information

Entry
Database: PDB / ID: 5bv8
TitleG1324S mutation in von Willebrand Factor A1 domain
Componentsvon Willebrand factor
KeywordsBLOOD CLOTTING / von Willebrand Factor / Platelet adhesion / VWFA
Function / homology
Function and homology information


Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / Weibel-Palade body / 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 / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / Weibel-Palade body / 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 / 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 / collagen-containing extracellular matrix / 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 / 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, 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 / 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. / 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 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsCampbell, J.C. / Kim, C. / Tischer, A. / Auton, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Mutational Constraints on Local Unfolding Inhibit the Rheological Adaptation of von Willebrand Factor.
Authors: Tischer, A. / Campbell, J.C. / Machha, V.R. / Moon-Tasson, L. / Benson, L.M. / Sankaran, B. / Kim, C. / Auton, M.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Dec 7, 2016Group: Database references / Other
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3063
Polymers28,2091
Non-polymers982
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.450, 86.450, 68.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein von Willebrand factor / / vWF


Mass: 28208.520 Da / Num. of mol.: 1 / Fragment: A1 domain (UNP residues 1238-1471) / Mutation: G1324S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VWF, F8VWF / Production host: Escherichia coli (E. coli) / References: UniProt: P04275
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5 / Details: 30% PEG 400, 100 mM CAPS/Sodium hydroxide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2014
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.59→43.23 Å / Num. obs: 38781 / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C29

4c29


Resolution: 1.59→43.23 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1997 5.16 %Random selection
Rwork0.163 ---
obs0.164 38736 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 5 232 1874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061688
X-RAY DIFFRACTIONf_angle_d1.0212284
X-RAY DIFFRACTIONf_dihedral_angle_d13.199639
X-RAY DIFFRACTIONf_chiral_restr0.04262
X-RAY DIFFRACTIONf_plane_restr0.005294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5931-1.63290.31341440.27352627X-RAY DIFFRACTION100
1.6329-1.67710.25071410.25532578X-RAY DIFFRACTION100
1.6771-1.72640.23861450.23622616X-RAY DIFFRACTION100
1.7264-1.78210.24891360.22182611X-RAY DIFFRACTION100
1.7821-1.84580.23571440.20432623X-RAY DIFFRACTION100
1.8458-1.91970.26721380.18492618X-RAY DIFFRACTION100
1.9197-2.00710.18191410.16462627X-RAY DIFFRACTION100
2.0071-2.11290.17391420.15532632X-RAY DIFFRACTION100
2.1129-2.24530.17821470.15452598X-RAY DIFFRACTION100
2.2453-2.41870.15581390.15482633X-RAY DIFFRACTION100
2.4187-2.6620.20111430.15532618X-RAY DIFFRACTION100
2.662-3.04710.18531410.16152638X-RAY DIFFRACTION100
3.0471-3.83870.15691450.14132642X-RAY DIFFRACTION100
3.8387-43.24090.13941510.13942678X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.125-0.1919-0.46781.7314-0.27013.12230.0224-0.05480.1446-0.01660.0519-0.0129-0.2865-0.0489-0.08830.11020.0146-0.00660.0862-0.01680.128333.844710.0464-2.9029
23.2197-2.7781.97036.263-3.71875.3131-0.0275-0.1109-0.259-0.16270.26060.470.153-0.5723-0.31730.1083-0.0155-0.02320.1578-0.02090.2124.77483.0903-5.999
30.9051-0.0975-0.21761.6943-0.52531.8681-0.0034-0.0113-0.0312-0.07360.03850.12980.1518-0.2446-0.01890.1036-0.0261-0.01840.1116-0.01080.1529.70350.5278-5.976
41.25440.31150.1233.0049-0.02963.15770.0417-0.0007-0.14720.06560.0234-0.05540.2255-0.0407-0.04050.12310.0009-0.0150.0968-0.00330.139239.4699-7.3267-5.1243
51.5245-0.1687-0.81491.10180.62754.5407-0.00860.0174-0.12110.0132-0.0089-0.10710.07560.1758-0.00220.19520.0296-0.03370.16990.00530.171846.4492-4.03970.5304
62.46861.3762-2.80352.0518-1.90843.30190.1089-0.13480.0770.087-0.0147-0.1984-0.47150.417-0.14240.21240.0061-0.01730.1909-0.0290.246544.482710.52670.2924
73.6635-1.70763.24535.5142-3.47416.5003-0.04580.79941.0177-0.0863-0.6447-0.4801-0.82390.54280.72410.3670.0423-0.00120.24750.12860.33442.507216.3829-21.4854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1262 THROUGH 1321 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 1322 THROUGH 1336 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 1337 THROUGH 1377 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 1378 THROUGH 1416 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 1417 THROUGH 1442 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 1443 THROUGH 1459 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 1460 THROUGH 1469 )

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