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- PDB-1ijk: The von Willebrand Factor mutant (I546V) A1 domain-botrocetin Complex -

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Basic information

Entry
Database: PDB / ID: 1ijk
TitleThe von Willebrand Factor mutant (I546V) A1 domain-botrocetin Complex
Components
  • (Botrocetin) x 2
  • von Willebrand factor
KeywordsBLOOD CLOTTING/TOXIN / Dinucleotide-binding fold / C-type lectin fold / BLOOD CLOTTING-TOXIN COMPLEX
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) / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of intracellular signal transduction / immunoglobulin binding / 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 / integrin binding / blood coagulation / 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 / Platelet degranulation / protein-folding chaperone binding / : / toxin activity / 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 / 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
von Willebrand factor / Snaclec botrocetin subunit alpha / Snaclec botrocetin subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Bothrops jararaca (jararaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFukuda, K. / Doggett, T.A. / Bankston, L.A. / Cruz, M.A. / Diacovo, T.G. / Liddington, R.C.
Citation
Journal: Structure / Year: 2002
Title: Structural basis of von Willebrand factor activation by the snake toxin botrocetin.
Authors: Fukuda, K. / Doggett, T.A. / Bankston, L.A. / Cruz, M.A. / Diacovo, T.G. / Liddington, R.C.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: Crystal structure of the von Willebrand factor A1 domain and implications for the binding of platelet glycoprotein Ib
Authors: Emsley, J. / Cruz, M. / Handin, R. / Liddington, R.
History
DepositionApr 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,4103
Polymers53,4103
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.664, 66.672, 69.402
Angle α, β, γ (deg.)90.00, 105.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein von Willebrand factor


Mass: 23125.789 Da / Num. of mol.: 1 / Fragment: A1 domain / Mutation: I546V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04275
#2: Protein Botrocetin


Mass: 15233.202 Da / Num. of mol.: 1 / Fragment: a-subunit / Source method: isolated from a natural source / Source: (natural) Bothrops jararaca (jararaca) / Secretion: venom / References: UniProt: P22029
#3: Protein Botrocetin


Mass: 15050.676 Da / Num. of mol.: 1 / Fragment: b-subunit / Source method: isolated from a natural source / Source: (natural) Bothrops jararaca (jararaca) / Secretion: venom / References: UniProt: P22030
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Fragment: Water / 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: 2.85 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
20.1 Msodium citrate1reservoirpH5.6
316 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 111 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.989 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. all: 18716 / Num. obs: 18178 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.9
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.207 / % possible all: 62.5
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 49341
Reflection shell
*PLUS
% possible obs: 62.5 % / Num. unique obs: 594 / Mean I/σ(I) obs: 5.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1281188.06 / Data cutoff high rms absF: 1281188.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 746 4.9 %RANDOM
Rwork0.219 ---
obs0.219 15258 92.7 %-
all-18204 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 94.79 Å2 / ksol: 0.9 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1--10.73 Å20 Å2-0.16 Å2
2--15.41 Å20 Å2
3----4.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 0 94 3760
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 2.6→2.66 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 41 4.4 %
Rwork0.254 2215 -
obs-937 62.5 %
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 6 Å / Num. reflection obs: 14512 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Highest resolution: 2.6 Å

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