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- PDB-1oak: CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR (VWF) A1 DOMAIN IN... -

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Basic information

Entry
Database: PDB / ID: 1oak
TitleCRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR (VWF) A1 DOMAIN IN COMPLEX WITH THE FUNCTION BLOCKING NMC-4 FAB
Components
  • (NMC-4 IGG1) x 2
  • VON WILLEBRAND FACTOR
KeywordsCOMPLEX (WILLEBRAND/IMMUNOGLOBULIN) / VON WILLEBRAND FACTOR / GLYCOPROTEIN IBA (A:ALPHA) BINDING / COMPLEX (WILLEBRAND-IMMUNOGLOBULIN) / BLOOD COAGULATION / COMPLEX (WILLEBRAND-IMMUNOGLOBULIN) 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 / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin ...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 / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / 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 / immunoglobulin mediated immune response / positive regulation of intracellular signal transduction / immunoglobulin binding / complement activation, classical pathway / Integrin cell surface interactions / antigen binding / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / positive regulation of phagocytosis / platelet alpha granule lumen / B cell differentiation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of immune response / 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 / antibacterial humoral response / Platelet degranulation / protein-folding chaperone binding / : / protease binding / cell adhesion / defense response to bacterium / external side of plasma membrane / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / cytoplasm
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 / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / : / von Willebrand factor A-like domain superfamily / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / : / Ig gamma-1 chain C region secreted form / von Willebrand factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIR / Resolution: 2.2 Å
AuthorsCelikel, R. / Varughese, K.I.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of the von Willebrand factor A1 domain in complex with the function blocking NMC-4 Fab.
Authors: Celikel, R. / Varughese, K.I. / Madhusudan / Yoshioka, A. / Ware, J. / Ruggeri, Z.M.
#1: Journal: Blood Cells Mol.Dis. / Year: 1997
Title: Crystal Structure of Nmc-4 Fab Anti-Von Willebrand Factor A1 Domain
Authors: Celikel, R. / Madhusudan / Varughese, K.I. / Shima, M. / Yoshioka, A. / Ware, J. / Ruggeri, Z.M.
History
DepositionDec 18, 1997Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: NMC-4 IGG1
H: NMC-4 IGG1
A: VON WILLEBRAND FACTOR


Theoretical massNumber of molelcules
Total (without water)69,7933
Polymers69,7933
Non-polymers00
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.200, 61.900, 72.900
Angle α, β, γ (deg.)90.00, 108.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody NMC-4 IGG1


Mass: 23461.805 Da / Num. of mol.: 1
Fragment: FAB FRAGMENT, AN ANTI VON WILLEBRAND FACTOR (VWF) A1 DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE ANTIBODY HEAVY CHAIN CONSISTS OF TWO SEGMENTS, H1 AND H2, BOTH LABELED CHAIN H IN THIS ENTRY
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Organ: BLOOD / Cell line (production host): MOPC21 / Production host: Mus musculus (house mouse) / References: GenBank: 1890296
#2: Antibody NMC-4 IGG1


Mass: 23887.551 Da / Num. of mol.: 1
Fragment: FAB FRAGMENT, AN ANTI VON WILLEBRAND FACTOR (VWF) A1 DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE ANTIBODY HEAVY CHAIN CONSISTS OF TWO SEGMENTS, H1 AND H2, BOTH LABELED CHAIN H IN THIS ENTRY
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Organ: BLOOD / Cell line (production host): MOPC21 / Production host: Mus musculus (house mouse) / References: GenBank: 1890294, UniProt: P01868*PLUS
#3: Protein VON WILLEBRAND FACTOR


Mass: 22444.135 Da / Num. of mol.: 1
Fragment: A1 DOMAIN RESIDUES 507 - 702, OR GLYCOPROTEIN IBA (A\:ALPHA) BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: BLOOD / Plasmid: PET8C / Production host: Escherichia coli (E. coli) / References: UniProt: P04275
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 3.1 Å3/Da / Density % sol: 64 %
Crystal growpH: 8 / Details: pH 8

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: PT COATED SI FLAT MIRROR BENT FOR VERTICAL FOCUS
RadiationMonochromator: BENT CYLINDRICAL GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 44346 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.048 / Net I/σ(I): 18.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 6.4 / % possible all: 98.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MIR / Resolution: 2.2→50 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.274 1610 4 %
Rwork0.201 --
obs0.201 44346 99 %
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-11.9 Å20 Å20 Å2
2---17.3 Å20 Å2
3---5.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5241 0 0 366 5607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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