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- PDB-3hob: Factor VIII Trp2313-His2315 segment is involved in membrane bindi... -

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Basic information

Entry
Database: PDB / ID: 3hob
TitleFactor VIII Trp2313-His2315 segment is involved in membrane binding as shown by crystal structure of complex between factor VIII C2 domain and an inhibitor
ComponentsCoagulation factor VIII
KeywordsBLOOD CLOTTING / Acute phase / Blood coagulation / Calcium / Disease mutation / Disulfide bond / Glycoprotein / Hemophilia / Metal-binding / Pharmaceutical / Polymorphism / Secreted / Sulfation
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 / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Coagulation factor VIII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsLiu, Z. / Yuan, C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Trp2313-His2315 of factor VIII C2 domain is involved in membrane binding: structure of a complex between the C2 domain and an inhibitor of membrane binding.
Authors: Liu, Z. / Lin, L. / Yuan, C. / Nicolaes, G.A. / Chen, L. / Meehan, E.J. / Furie, B. / Furie, B. / Huang, M.
History
DepositionJun 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Coagulation factor VIII
A: Coagulation factor VIII


Theoretical massNumber of molelcules
Total (without water)36,0592
Polymers36,0592
Non-polymers00
Water81145
1
M: Coagulation factor VIII


Theoretical massNumber of molelcules
Total (without water)18,0301
Polymers18,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Coagulation factor VIII


Theoretical massNumber of molelcules
Total (without water)18,0301
Polymers18,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.279, 58.988, 60.086
Angle α, β, γ (deg.)90.00, 110.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Coagulation factor VIII / Factor VIIIa light chain


Mass: 18029.559 Da / Num. of mol.: 2 / Fragment: factor VIII c2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F8, F8C / Plasmid: pPIC9K / Production host: pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P00451
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.99 Å3/Da / Density % sol: 38.15 % / Mosaicity: 0.534 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30.0% PEG 2000, MME 0.15M KBr, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.04 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 2, 2009 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 1231 / Num. obs: 17899 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.084 / Χ2: 0.938 / Net I/σ(I): 13.492
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.415 / Num. unique all: 1231 / Χ2: 0.34 / % possible all: 63.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D7P

1d7p


Resolution: 2.07→33.39 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.853 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26278 840 5 %RANDOM
Rwork0.21742 ---
obs0.21966 15895 96.26 %-
all-15895 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.96 Å2 / Biso mean: 28.036 Å2 / Biso min: 12.71 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.07→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 0 45 2529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222638
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9263592
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1445328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13924.034119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42715456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2371513
X-RAY DIFFRACTIONr_chiral_restr0.1160.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022010
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21042
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21779
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3530.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1361.51650
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42522605
X-RAY DIFFRACTIONr_scbond_it2.08831153
X-RAY DIFFRACTIONr_scangle_it3.0044.5982
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 48 -
Rwork0.232 952 -
obs--79.18 %

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