[English] 日本語
Yorodumi- PDB-1iqd: Human Factor VIII C2 Domain complexed to human monoclonal BO2C11 Fab. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iqd | ||||||
---|---|---|---|---|---|---|---|
Title | Human Factor VIII C2 Domain complexed to human monoclonal BO2C11 Fab. | ||||||
Components |
| ||||||
Keywords | IMMUNE 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 / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Spiegel 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1iqd.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1iqd.ent.gz | 101.3 KB | Display | PDB format |
PDBx/mmJSON format | 1iqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iqd_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1iqd_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 1iqd_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 1iqd_validation.cif.gz | 40.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/1iqd ftp://data.pdbj.org/pub/pdb/validation_reports/iq/1iqd | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 22920.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Strain: BO2C11 |
---|---|
#2: Antibody | Mass: 22738.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Strain: BO2C11 |
#3: Protein | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.62 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 10, 2000 |
Radiation | Monochromator: ALS 5.0.2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method 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
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.966 Å2 / ksol: 0.361134 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.58 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.271 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.213 |