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- PDB-1u0o: The mouse von Willebrand Factor A1-botrocetin complex -

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Basic information

Entry
Database: PDB / ID: 1u0o
TitleThe mouse von Willebrand Factor A1-botrocetin complex
Components
  • (Botrocetin) x 2
  • von Willebrand factor
KeywordsBLOOD CLOTTING / Rossmann fold / C-type lectin fold / Protein-protein complex
Function / homology
Function and homology information


GP1b-IX-V activation signalling / Platelet Aggregation (Plug Formation) / Intrinsic Pathway of Fibrin Clot Formation / Platelet Adhesion to exposed collagen / activation of blood coagulation via clotting cascade / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / MAP2K and MAPK activation / Weibel-Palade body ...GP1b-IX-V activation signalling / Platelet Aggregation (Plug Formation) / Intrinsic Pathway of Fibrin Clot Formation / Platelet Adhesion to exposed collagen / activation of blood coagulation via clotting cascade / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / MAP2K and MAPK activation / Weibel-Palade body / Integrin cell surface interactions / hemostasis / Platelet degranulation / cell-substrate adhesion / immunoglobulin binding / collagen binding / placenta development / liver development / platelet activation / integrin binding / blood coagulation / protein-folding chaperone binding / : / toxin activity / protease binding / cell adhesion / inflammatory response / external side of plasma membrane / endoplasmic reticulum / extracellular space / 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 / von Willebrand factor type C domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / 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 / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / von Willebrand factor type A domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Snaclec botrocetin subunit alpha / Snaclec botrocetin subunit beta / von Willebrand factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bothrops jararaca (jararaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFukuda, K. / Liddington, R.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The snake venom protein botrocetin acts as a biological brace to promote dysfunctional platelet aggregation
Authors: Fukuda, K. / Doggett, T. / Laurenzi, I.J. / Liddington, R.C. / Diacovo, T.G.
History
DepositionJul 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botrocetin
B: Botrocetin
C: von Willebrand factor


Theoretical massNumber of molelcules
Total (without water)53,8463
Polymers53,8463
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.338, 73.660, 114.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Botrocetin / Platelet coagglutinin


Mass: 15233.202 Da / Num. of mol.: 1 / Fragment: Alpha chain / Source method: isolated from a natural source / Source: (natural) Bothrops jararaca (jararaca) / Secretion: venom / References: UniProt: P22029
#2: Protein Botrocetin / Platelet coagglutinin


Mass: 15050.676 Da / Num. of mol.: 1 / Fragment: Beta chain / Source method: isolated from a natural source / Source: (natural) Bothrops jararaca (jararaca) / Secretion: venom / References: UniProt: P22030
#3: Protein von Willebrand factor


Mass: 23562.441 Da / Num. of mol.: 1 / Fragment: VWF A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: VwF / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CIZ8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 5000 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 7, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.7→200 Å / Num. all: 13814 / Num. obs: 12759 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.1
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.5 / % possible all: 79.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→6 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 290750.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 574 5.1 %RANDOM
Rwork0.218 ---
obs0.218 11310 92 %-
all-12292 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 104.424 Å2 / ksol: 0.843028 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1--14.24 Å20 Å20 Å2
2--2.08 Å20 Å2
3---12.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3689 0 0 39 3728
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it1.712
X-RAY DIFFRACTIONc_scangle_it2.622.5
LS refinement shellResolution: 2.7→2.85 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 84 5.1 %
Rwork0.32 1552 -
obs--81 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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