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- PDB-1iqd: Human Factor VIII C2 Domain complexed to human monoclonal BO2C11 Fab. -

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Basic information

Entry
Database: PDB / ID: 1iqd
TitleHuman Factor VIII C2 Domain complexed to human monoclonal BO2C11 Fab.
Components
  • HUMAN FACTOR VIII
  • HUMAN MONOCLONAL BO2C11 FAB HEAVY CHAIN
  • HUMAN MONOCLONAL BO2C11 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM/BLOOD CLOTTING / FACTOR VIII / C2 DOMAIN / ANTIBODY / BLOOD COAGULATION / INHIBITOR / BO2C11 / IMMUNE SYSTEM-BLOOD CLOTTING COMPLEX
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 / endoplasmic reticulum-Golgi intermediate compartment membrane / Intrinsic Pathway of Fibrin Clot Formation / platelet alpha granule lumen / acute-phase response / Golgi lumen / blood coagulation / Platelet degranulation / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSpiegel Jr., P.C. / Jacquemin, M. / Saint-Remy, J.M. / Stoddard, B.L. / Pratt, K.P.
Citation
Journal: Blood / Year: 2001
Title: Structure of a factor VIII C2 domain-immunoglobulin G4kappa Fab complex: identification of an inhibitory antibody epitope on the surface of factor VIII.
Authors: Spiegel Jr., P.C. / Jacquemin, M. / Saint-Remy, J.M. / Stoddard, B.L. / Pratt, K.P.
#1: Journal: Nature / Year: 1999
Title: Structure of the C2 domain of human factor VIII at 1.5 A resolution
Authors: Pratt, K.P. / Shen, B.W. / Takeshima, K. / Davie, E.W. / Fujikawa, K. / Stoddard, B.L.
#2: Journal: Blood / Year: 2000
Title: Hemophilic factor VIII C1- and C2-domain missense mutations and their modeling to the 1.5-angstrom human C2-domain crystal structure
Authors: Liu, M.L. / Shen, B.W. / Nakaya, S. / Pratt, K.P. / Fujikawa, K. / Davie, E.W. / Stoddard, B.L. / Thompson, A.R.
History
DepositionJul 21, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN MONOCLONAL BO2C11 FAB LIGHT CHAIN
B: HUMAN MONOCLONAL BO2C11 FAB HEAVY CHAIN
C: HUMAN FACTOR VIII


Theoretical massNumber of molelcules
Total (without water)63,4033
Polymers63,4033
Non-polymers00
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-34 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.535, 73.701, 112.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody HUMAN MONOCLONAL BO2C11 FAB LIGHT CHAIN


Mass: 22920.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Strain: BO2C11
#2: Antibody HUMAN MONOCLONAL BO2C11 FAB HEAVY CHAIN


Mass: 22738.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Strain: BO2C11
#3: Protein HUMAN FACTOR VIII / / COAGULATION FACTOR VII


Mass: 17744.326 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN / Mutation: S2296C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P00451
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG8000, sodium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMHEPES1drop
20.1 M1dropNaCl
310 mg/mlprotein1drop
416 %PEG80001reservoir
50.1 MHEPES1reservoir
60.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 10, 2000
RadiationMonochromator: ALS 5.0.2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 284482 / Num. obs: 284362 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.9 Å2
Reflection shellResolution: 2→2.03 Å / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 36867 / Redundancy: 7.7 % / Num. measured all: 284482 / Rmerge(I) obs: 0.061

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
XFITdata reduction
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.58 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 225052.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3566 9.9 %RANDOM
Rwork0.203 ---
all-35941 --
obs-35941 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.966 Å2 / ksol: 0.361134 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å20 Å20 Å2
2---1.19 Å20 Å2
3----1.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4335 0 0 477 4812
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 524 9.4 %
Rwork0.213 5068 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.271 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.213

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