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- PDB-1fns: CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR (VWF) A1 DOMAIN I5... -

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Basic information

Entry
Database: PDB / ID: 1fns
TitleCRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR (VWF) A1 DOMAIN I546V MUTANT IN COMPLEX WITH THE FUNCTION BLOCKING FAB NMC4
Components
  • (IMMUNOGLOBULIN NMC-4 IGG1) x 2
  • VON WILLEBRAND FACTOR
KeywordsIMMUNE SYSTEM / VON WILLEBRAND FACTOR / GLYCOPROTEIN IBA (A:ALPHA) BINDING / COMPLEX (WILLEBRAND-IMMUNOGLOBULIN) / BLOOD COAGULATION TYPE 2B VON WILLEBRAND DISEASE
Function / homology
Function and homology information


Weibel-Palade body / Defective F8 binding to von Willebrand factor / hemostasis / humoral immune response mediated by circulating immunoglobulin / Platelet Adhesion to exposed collagen / phagocytosis, recognition / platelet alpha granule / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity ...Weibel-Palade body / Defective F8 binding to von Willebrand factor / hemostasis / humoral immune response mediated by circulating immunoglobulin / Platelet Adhesion to exposed collagen / phagocytosis, recognition / platelet alpha granule / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / positive regulation of intracellular signal transduction / phagocytosis, engulfment / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / immunoglobulin complex, circulating / cell-substrate adhesion / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin binding / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / GRB2:SOS provides linkage to MAPK signaling for Integrins / immunoglobulin mediated immune response / Integrin cell surface interactions / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / extracellular matrix / Integrin signaling / B cell differentiation / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / 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 / positive regulation of immune response / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / antibacterial humoral response / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / cell adhesion / defense response to bacterium / external side of plasma membrane / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytoplasm
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. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / 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 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Ig gamma-1 chain C region secreted form / von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsVarughese, K.I.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: von Willebrand factor conformation and adhesive function is modulated by an internalized water molecule.
Authors: Celikel, R. / Ruggeri, Z.M. / Varughese, K.I.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal Structure of the Von Willebrand Factor A1 D Domain in Complex with the Function Blocking Nmc-4 DOMAIN IN COMPLEX WITH THE FUNCTION BLOCKING NMC-4 FAB
Authors: Celikel, R. / Varughese, K.I. / Madhusudan / Yoshioka, A. / Ware, J. / Ruggeri, Z.M.
History
DepositionAug 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,2303
Polymers70,2303
Non-polymers00
Water11,458636
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.396, 62.673, 73.789
Angle α, β, γ (deg.)90.00, 108.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1226-

HOH

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Components

#1: Antibody IMMUNOGLOBULIN NMC-4 IGG1


Mass: 23694.061 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT, LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA CELLS, MOPC21 CELLS / References: UniProt: P01837*PLUS
#2: Antibody IMMUNOGLOBULIN NMC-4 IGG1


Mass: 24105.848 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT, HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA CELLS, MOPC21 CELLS / References: UniProt: P01868*PLUS
#3: Protein VON WILLEBRAND FACTOR /


Mass: 22430.107 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) / Plasmid: PET8C / Production host: Escherichia coli (E. coli) / References: UniProt: P04275
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 636 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
260 mMcalcium acetate1drop
312 %(w/v)mPEG50001reservoir
40.12 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 23.5 Å2
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 57228 / % possible obs: 93.2 % / Num. measured all: 175343 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 82.4 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.3

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Processing

SoftwareName: CNS / Version: 0.4 / Classification: refinement
RefinementResolution: 2→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 666370.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1139 2.3 %RANDOM
Rwork0.172 ---
obs0.172 49150 80 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.94 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.96 Å20 Å2-0.09 Å2
2--5.52 Å20 Å2
3----1.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 0 0 636 5536
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 136 2.3 %
Rwork0.208 5706 -
obs--57.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22

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