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- PDB-1uex: Crystal structure of von Willebrand Factor A1 domain complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1uex
TitleCrystal structure of von Willebrand Factor A1 domain complexed with snake venom bitiscetin
Components
  • bitiscetin alpha chain
  • bitiscetin beta chain
  • von Willebrand Factor
KeywordsTOXIN/BLOOD CLOTTING / C-type lectin heterodimer / TOXIN-BLOOD CLOTTING 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 / Defective F8 cleavage by thrombin / cell-substrate adhesion / 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 / 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 bitiscetin subunit alpha / Snaclec bitiscetin subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Bitis arietans (puff adder)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMaita, N. / Nishio, K. / Nishimoto, E. / Matsui, T. / Shikamoto, Y. / Morita, T. / Sadler, J.E. / Mizuno, H.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of von Willebrand factor A1 domain complexed with snake venom, bitiscetin. Insight into glycoprotein Ibalpha binding mechanism induced by snake venom proteins.
Authors: Maita, N. / Nishio, K. / Nishimoto, E. / Matsui, T. / Shikamoto, Y. / Morita, T. / Sadler, J.E. / Mizuno, H.
History
DepositionMay 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bitiscetin alpha chain
B: bitiscetin beta chain
C: von Willebrand Factor


Theoretical massNumber of molelcules
Total (without water)53,6653
Polymers53,6653
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.282, 89.282, 53.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein bitiscetin alpha chain / alpha-subunit


Mass: 14953.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bitis arietans (puff adder) / Secretion: venom / References: GenBank: 2134244, UniProt: Q7LZK5*PLUS
#2: Protein bitiscetin beta chain / beta-subunit


Mass: 14822.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bitis arietans (puff adder) / Secretion: venom / References: GenBank: 2134245, UniProt: Q7LZK8*PLUS
#3: Protein von Willebrand Factor / vWF


Mass: 23889.627 Da / Num. of mol.: 1 / Fragment: A1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04275
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.06 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 10% PEG 6000, 2% PEG-MME 550, 5% MPD, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
20.1 Msodium HEPES1reservoirpH7.5
310 %PEG60001reservoir
45 %MPD1reservoir
50.1 MBicine-Na1reservoirpH9.0
620 %PEG550 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 9672 / % possible obs: 91.6 % / Redundancy: 5.6 % / Rsym value: 0.107
Reflection shellResolution: 2.85→2.99 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.31 / % possible all: 91.6
Reflection
*PLUS
Num. obs: 9055 / Num. measured all: 51631 / Rmerge(I) obs: 0.107
Reflection shell
*PLUS
% possible obs: 91.6 % / Num. unique obs: 1456 / Num. measured obs: 8285 / Rmerge(I) obs: 0.311

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JWI and 1AUQ

1jwi

1auq


Resolution: 2.85→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.276 1110 RANDOM
Rwork0.194 --
all-9991 -
obs-9163 -
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 0 40 3691
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_dihedral_angle_d22.85
X-RAY DIFFRACTIONc_improper_angle_d0.68
Refinement
*PLUS
% reflection Rfree: 12 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0052
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.85
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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