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- PDB-7kbt: Factor VIII in complex with the anti-C2 domain antibody, G99 -

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Basic information

Entry
Database: PDB / ID: 7kbt
TitleFactor VIII in complex with the anti-C2 domain antibody, G99
Components
  • Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII
  • G99 heavy chain
  • G99 light chain
KeywordsBLOOD CLOTTING/Immune System / Antibody / inhibitor / BLOOD CLOTTING / BLOOD CLOTTING-Immune System 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 / 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, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / Coagulation factor VIII / Coagulation factor VIII
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.15 Å
AuthorsRonayne, E.K. / Gish, J. / Wilson, C. / Peters, S. / Spencer, H.T. / Spiegel, P.C. / Childers, K.C.
Funding support United States, 6items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MRI 1429164 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R15HL103518 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)U54HL141981 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R44HL117511 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R44HL110448 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)U54HL112309 United States
CitationJournal: Front Immunol / Year: 2021
Title: Structure of Blood Coagulation Factor VIII in Complex With an Anti-C2 Domain Non-Classical, Pathogenic Antibody Inhibitor
Authors: Ronayne, E.K. / Peters, S.C. / Gish, J.S. / Wilson, C. / Spencer, H.T. / Doering, C.B. / Lollar, P. / Spiegel, P.C. / Childers, K.C.
History
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: 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.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 18, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII
E: G99 heavy chain
F: G99 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,1199
Polymers215,8803
Non-polymers1,2396
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.243, 132.243, 380.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII / Procoagulant component / Antihemophilic factor / AHF / Procoagulant component / Procoagulant ...Procoagulant component / Antihemophilic factor / AHF / Procoagulant component / Procoagulant component / Procoagulant component / Antihemophilic factor / AHF / Procoagulant component


Mass: 168287.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig), (gene. exp.) Homo sapiens (human)
Gene: F8, CF8, F8, F8C / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P12263, UniProt: P00451

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Antibody , 2 types, 2 molecules EF

#2: Antibody G99 heavy chain


Mass: 23952.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody G99 light chain


Mass: 23640.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Sugars , 2 types, 3 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 3 molecules

#6: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestN
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: 3.85 Å3/Da / Density % sol: 68.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 8 - 18% PEG 1500, PEG 6K, or PEG 10K and 50mM malic acid, pH 7.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.15→25.48 Å / Num. obs: 26284 / % possible obs: 99.08 % / Redundancy: 2 % / Biso Wilson estimate: 195.91 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.06373 / Rpim(I) all: 0.06373 / Rrim(I) all: 0.09012 / Net I/σ(I): 6.31
Reflection shellResolution: 4.15→4.298 Å / Redundancy: 2 % / Rmerge(I) obs: 1.359 / Mean I/σ(I) obs: 0.48 / Num. unique obs: 2546 / CC1/2: 0.373 / CC star: 0.737 / Rpim(I) all: 1.359 / Rrim(I) all: 1.922 / % possible all: 98.31

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
Adxvdata reduction
XDSdata reduction
PHASERphasing
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MF0

6mf0


Resolution: 4.15→25.48 Å / SU ML: 0.9 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3384 1987 7.58 %
Rwork0.2998 --
obs0.302 26198 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.15→25.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11293 0 73 0 11366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511679
X-RAY DIFFRACTIONf_angle_d1.07415822
X-RAY DIFFRACTIONf_dihedral_angle_d11.2216880
X-RAY DIFFRACTIONf_chiral_restr0.0591726
X-RAY DIFFRACTIONf_plane_restr0.0082022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.15-4.25340.44661370.47481652X-RAY DIFFRACTION98
4.2534-4.36780.43361370.45731681X-RAY DIFFRACTION100
4.3678-4.49570.4371390.42571693X-RAY DIFFRACTION100
4.4957-4.640.41511400.38371694X-RAY DIFFRACTION100
4.64-4.80480.38971390.36071705X-RAY DIFFRACTION100
4.8048-4.99580.38471400.35311708X-RAY DIFFRACTION100
4.9958-5.22140.43911410.34051712X-RAY DIFFRACTION100
5.2214-5.49410.39241430.32831743X-RAY DIFFRACTION100
5.4941-5.83460.35541390.32651702X-RAY DIFFRACTION100
5.8346-6.2790.34061430.3311753X-RAY DIFFRACTION100
6.279-6.89980.33831430.32081734X-RAY DIFFRACTION100
6.8998-7.87310.3361440.29481759X-RAY DIFFRACTION100
7.8731-9.82640.30261470.26741794X-RAY DIFFRACTION100
9.8264-25.480.30291550.22581883X-RAY DIFFRACTION99

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