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- PDB-4ki5: Cystal structure of human factor VIII C2 domain in a ternary comp... -

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Basic information

Entry
Database: PDB / ID: 4ki5
TitleCystal structure of human factor VIII C2 domain in a ternary complex with murine inhbitory antibodies 3E6 and G99
Components
  • (MURINE MONOCLONAL 3E6 FAB ...) x 2
  • (MURINE MONOCLONAL G99 FAB ...) x 2
  • Coagulation factor VIII
KeywordsIMMUNE SYSTEM / immunoglobulin fold / discoidin fold / antibody / blood coagulation factor / antigen binding / blood plasma
Function / homology
Function and homology information


Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 sulfation at Y1699 / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant ...Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 sulfation at Y1699 / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Defective F8 cleavage by thrombin / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Golgi lumen / blood coagulation / Platelet degranulation / signaling receptor activity / oxidoreductase activity / copper ion binding / endoplasmic reticulum lumen / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Multicopper oxidase, C-terminal / Multicopper oxidase / F5/8 type C domain ...Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Multicopper oxidase, C-terminal / Multicopper oxidase / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Multicopper oxidase, N-terminal / Multicopper oxidase / Galactose-binding domain-like / Cupredoxin / Galactose-binding-like domain superfamily / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Coagulation factor VIII
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.47 Å
AuthorsWalter, J.D. / Meeks, S.L. / Healey, J.F. / Lollar, P. / Spiegel, P.C.
CitationJournal: Blood / Year: 2013
Title: Structure of the factor VIII C2 domain in a ternary complex with 2 inhibitor antibodies reveals classical and nonclassical epitopes.
Authors: Walter, J.D. / Werther, R.A. / Brison, C.M. / Cragerud, R.K. / Healey, J.F. / Meeks, S.L. / Lollar, P. / Spiegel, P.C.
History
DepositionMay 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: MURINE MONOCLONAL 3E6 FAB HEAVY CHAIN
D: MURINE MONOCLONAL 3E6 FAB LIGHT CHAIN
E: MURINE MONOCLONAL G99 FAB HEAVY CHAIN
F: MURINE MONOCLONAL G99 FAB LIGHT CHAIN
M: Coagulation factor VIII


Theoretical massNumber of molelcules
Total (without water)115,1985
Polymers115,1985
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.250, 71.160, 277.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Antibody , 4 types, 4 molecules CDEF

#1: Antibody MURINE MONOCLONAL 3E6 FAB HEAVY CHAIN


Mass: 23538.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody MURINE MONOCLONAL 3E6 FAB LIGHT CHAIN


Mass: 23330.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody MURINE MONOCLONAL G99 FAB HEAVY CHAIN


Mass: 23952.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Antibody MURINE MONOCLONAL G99 FAB LIGHT CHAIN


Mass: 23640.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Protein / Non-polymers , 2 types, 268 molecules M

#5: Protein Coagulation factor VIII / Antihemophilic factor / AHF / Procoagulant component / Factor VIIIa heavy chain / 200 kDa isoform / ...Antihemophilic factor / AHF / Procoagulant component / Factor VIIIa heavy chain / 200 kDa isoform / Factor VIIIa heavy chain / 92 kDa isoform / Factor VIII B chain / Factor VIIIa light chain


Mass: 20736.582 Da / Num. of mol.: 1 / Fragment: C2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F8, F8C / Production host: Escherichia coli (E. coli) / References: UniProt: P00451
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG-1000, 0.15 M sodium acetate, 0.025 M Tris-HCl, 0.05 M NaCl, 0.15 M ammonium nitrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.47→56.428 Å / Num. all: 39550 / Num. obs: 39550 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 %
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.47-2.6113.90.840.97838856390.8499.7
2.61-2.7614.10.5651.47533453390.56599.7
2.76-2.9614.20.3931.97186950760.39399.9
2.96-3.1914.20.272.86725847510.27100
3.19-3.514.10.1983.76137643420.198100
3.5-3.9114.10.1534.55662640080.153100
3.91-4.52140.10964980135460.109100
4.52-5.53140.097.24218830240.09100
5.53-7.8213.70.0936.73294924020.093100
7.82-56.42812.60.0668.51788514230.06699.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å56.43 Å
Translation2.5 Å56.43 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
PHENIX1.8_1069refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→56.428 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / σ(F): 0 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1998 5.06 %RANDOM
Rwork0.1877 ---
obs0.1903 39480 99.76 %-
all-39575 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.13 Å2 / Biso mean: 51.1305 Å2 / Biso min: 24.69 Å2
Refinement stepCycle: LAST / Resolution: 2.47→56.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7807 0 0 267 8074

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