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- PDB-1sq0: Crystal Structure of the Complex of the Wild-type Von Willebrand ... -

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Basic information

Entry
Database: PDB / ID: 1sq0
TitleCrystal Structure of the Complex of the Wild-type Von Willebrand Factor A1 domain and Glycoprotein Ib alpha at 2.6 Angstrom Resolution
Components
  • Platelet glycoprotein Ib alpha chain (Glycoprotein Ibalpha) (GP-Ib alpha) (GPIbA) (GPIb-alpha) (CD42B-alpha) (CD42B) [Contains: Glycocalicin]
  • Von Willebrand factor (vWF) [Contains: Von Willebrand antigen II]
KeywordsBLOOD CLOTTING / Leucine Rich Repeat (LRR) / right-handed beta-alpha superhelix) / Integrin A (or I) domain fold
Function / homology
Function and homology information


thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Weibel-Palade body / Defective F8 binding to von Willebrand factor / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / hemostasis / Defective F9 activation / Platelet Adhesion to exposed collagen / platelet alpha granule ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Weibel-Palade body / Defective F8 binding to von Willebrand factor / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / hemostasis / Defective F9 activation / Platelet Adhesion to exposed collagen / platelet alpha granule / positive regulation of platelet activation / positive regulation of intracellular signal transduction / megakaryocyte development / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / regulation of blood coagulation / immunoglobulin binding / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / release of sequestered calcium ion into cytosol / collagen binding / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / extracellular matrix / Integrin signaling / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / cell morphogenesis / 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 surface receptor signaling pathway / cell adhesion / external side of plasma membrane / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
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. / Leucine rich repeat N-terminal domain / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Leucine-rich repeats, bacterial type / von Willebrand factor, type A domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / von Willebrand factor type A domain / Alpha-Beta Horseshoe / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / von Willebrand factor, type A / Leucine-rich repeat profile. / von Willebrand factor A-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
von Willebrand factor / Platelet glycoprotein Ib alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsDumas, J.J. / Kumar, R. / McDonagh, T. / Sullivan, F. / Stahl, M.L. / Somers, W.S. / Mosyak, L.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of the wild-type von Willebrand factor A1-glycoprotein Ibalpha complex reveals conformation differences with a complex bearing von Willebrand disease mutations
Authors: Dumas, J.J. / Kumar, R. / McDonagh, T. / Sullivan, F. / Stahl, M.L. / Somers, W.S. / Mosyak, L.
#1: Journal: Science / Year: 2003
Title: Crystal Structure of the GpIb(alpha)-Thrombin Complex Essential for Platelet Aggregation
Authors: Dumas, J.J. / Kumar, R. / Seehra, J. / Somers, W.S. / Mosyak, L.
History
DepositionMar 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE ASN RESIDUES AT POSITIONS 21 AND 159 OF CHAIN B, WHICH ARE SITES FOR N-LINKED ...SEQUENCE ASN RESIDUES AT POSITIONS 21 AND 159 OF CHAIN B, WHICH ARE SITES FOR N-LINKED GLYCOSYLATION, WERE MUTATED TO ASP.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Von Willebrand factor (vWF) [Contains: Von Willebrand antigen II]
B: Platelet glycoprotein Ib alpha chain (Glycoprotein Ibalpha) (GP-Ib alpha) (GPIbA) (GPIb-alpha) (CD42B-alpha) (CD42B) [Contains: Glycocalicin]


Theoretical massNumber of molelcules
Total (without water)56,5512
Polymers56,5512
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.497, 116.104, 67.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Von Willebrand factor (vWF) [Contains: Von Willebrand antigen II]


Mass: 24466.361 Da / Num. of mol.: 1 / Fragment: A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VWF, F8VWF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P04275
#2: Protein Platelet glycoprotein Ib alpha chain (Glycoprotein Ibalpha) (GP-Ib alpha) (GPIbA) (GPIb-alpha) (CD42B-alpha) (CD42B) [Contains: Glycocalicin]


Mass: 32084.498 Da / Num. of mol.: 1 / Fragment: Glycoprotein Ib-(alpha) / Mutation: N21D, N159D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GP1BA / Cell (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P07359
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG-3350; potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.97942, 0.97959, 0.9686
SYNCHROTRONALS 5.0.221
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDAug 31, 2002
ADSC QUANTUM 42CCDMay 18, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double-crystal, Si(111)MADMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979591
30.96861
411
ReflectionResolution: 2.6→49.58 Å / Num. obs: 17150 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28.5 Å2
Reflection shellResolution: 2.6→2.75 Å / % possible all: 84

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→49.58 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 132767.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED RESIDUES IN CHAIN A INCLUDE N-TERMINAL RESIDUES 496-5 AND C-TERMINAL RESIDUES 704-709. IN CHAIN A, SIDE CHAIN FOR LYS IS DISORDERED. DISORDERED RESIDUES IN CHAIN B INCLUDE C-TERMINAL RESIDUES 266-288.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1685 9.8 %RANDOM
Rwork0.19 ---
obs0.19 17150 93.9 %-
all-17150 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.4256 Å2 / ksol: 0.305156 e/Å3
Displacement parametersBiso mean: 40.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å20 Å20 Å2
2---10.55 Å20 Å2
3---12.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 0 318 3982
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.622
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.582.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 248 9.9 %
Rwork0.281 2261 -
obs--84 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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