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- PDB-9d5d: Crystal Structure of Blood Coagulation Factor VIII C2 Domain Muta... -

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Basic information

Entry
Database: PDB / ID: 9d5d
TitleCrystal Structure of Blood Coagulation Factor VIII C2 Domain Mutant L2251A/L2252A
ComponentsFactor VIIIa light chain
KeywordsBLOOD CLOTTING / Blood coagulation factor VIII / lipid binding protein / factor VIII C2 domain mutant
Function / homology
Function and homology information


Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Defective F8 sulfation at Y1699 / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / 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 / Defective F8 sulfation at Y1699 / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / 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 ...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 / Cupredoxin / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Coagulation factor VIII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsAvery, N.G. / Childers, K.C. / Spiegel, P.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R15 HL135658 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)U54 HL141981 United States
CitationJournal: J.Thromb.Haemost. / Year: 2024
Title: Biophysical characterization of blood coagulation factor VIII binding to lipid nanodiscs that mimic activated platelet surfaces.
Authors: Avery, N.G. / Young, I.R. / Lu, S. / Vaughan, J.D. / Korus, P.S. / Richardson, T.N. / Childers, K.C. / Smirnov, S.L. / Spiegel Jr., P.C.
History
DepositionAug 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: Factor VIIIa light chain


Theoretical massNumber of molelcules
Total (without water)18,5631
Polymers18,5631
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.962, 49.962, 116.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Factor VIIIa light chain / Blood coagulation factor VIII


Mass: 18563.098 Da / Num. of mol.: 1 / Fragment: C2 domain (UNP residues 2191-2351) / Mutation: L2251A,L2252A
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.96 Å3/Da / Density % sol: 37.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 4 M potassium formate, 0.1 M Bis-Tris propane, pH 9, 2% w/v PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.83→37.93 Å / Num. obs: 13614 / % possible obs: 99.21 % / Redundancy: 20.8 % / Biso Wilson estimate: 20.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.032 / Rrim(I) all: 0.155 / Net I/σ(I): 15.3
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1248 / CC1/2: 0.841 / Rpim(I) all: 0.231 / Rrim(I) all: 0.73 / % possible all: 93.06

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Processing

Software
NameVersionClassification
PHENIXv1.21.1refinement
Cootv0.9.4model building
PHENIXv1.21.1phasing
APEXdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→37.93 Å / SU ML: 0.1935 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2669
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 1362 10 %
Rwork0.1864 12252 -
obs0.19 13614 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.93 Å2
Refinement stepCycle: LAST / Resolution: 1.83→37.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 0 156 1410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831286
X-RAY DIFFRACTIONf_angle_d1.06741745
X-RAY DIFFRACTIONf_chiral_restr0.0732190
X-RAY DIFFRACTIONf_plane_restr0.0056224
X-RAY DIFFRACTIONf_dihedral_angle_d17.0777468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.90.30091250.26041123X-RAY DIFFRACTION93.06
1.9-1.970.2471320.20151188X-RAY DIFFRACTION98.88
1.97-2.060.21871330.18311195X-RAY DIFFRACTION100
2.06-2.170.23221350.1781219X-RAY DIFFRACTION100
2.17-2.310.2761340.19471205X-RAY DIFFRACTION100
2.31-2.480.26571370.19841231X-RAY DIFFRACTION100
2.48-2.730.25621350.20671221X-RAY DIFFRACTION100
2.73-3.130.24171390.19041243X-RAY DIFFRACTION100
3.13-3.940.18961400.16261269X-RAY DIFFRACTION100
3.94-37.930.18041520.17931358X-RAY DIFFRACTION100

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