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- PDB-4pt6: The discobody: an engineered discoidin domain from factor VIII th... -

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Basic information

Entry
Database: PDB / ID: 4pt6
TitleThe discobody: an engineered discoidin domain from factor VIII that binds v 3 integrin with antibody-like affinities
ComponentsCoagulation factor VIII
KeywordsCELL ADHESION / Integrin binding / Integrin
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
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: 2.1 Å
AuthorsKym, G. / Shi, K. / Kamajaya, A. / Hamdouche, S. / Kostecki, J.S. / Wannier, T. / Li, B. / Nikolovski, P. / Mayo, S.L.
CitationJournal: To be Published
Title: The discobody: an engineered discoidin domain from factor VIII that binds v 3 integrin with antibody-like affinities
Authors: Kym, G. / Shi, K. / Kamajaya, A. / Hamdouche, S. / Kostecki, J.S. / Wannier, T. / Li, B. / Nikolovski, P. / Mayo, S.L.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor VIII
B: Coagulation factor VIII


Theoretical massNumber of molelcules
Total (without water)38,3422
Polymers38,3422
Non-polymers00
Water68538
1
A: Coagulation factor VIII


Theoretical massNumber of molelcules
Total (without water)19,1711
Polymers19,1711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Coagulation factor VIII


Theoretical massNumber of molelcules
Total (without water)19,1711
Polymers19,1711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.449, 38.446, 48.842
Angle α, β, γ (deg.)98.56, 91.77, 111.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Coagulation factor VIII / Antihemophilic factor / AHF / Procoagulant component / Factor VIIIa heavy chain / 200 kDa isoform / ...Antihemophilic factor / AHF / Procoagulant component / Factor VIIIa heavy chain / 200 kDa isoform / Factor VIIIa heavy chain / 92 kDa isoform / Factor VIII B chain / Factor VIIIa light chain


Mass: 19170.779 Da / Num. of mol.: 2 / Fragment: unp residues 2190-2351
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.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.46 Å3/Da / Density % sol: 15.79 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 11234

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→31.147 Å / SU ML: 0.25 / σ(F): 1.98 / Phase error: 33.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 587 5.23 %
Rwork0.1988 --
obs0.2016 11234 88.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→31.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 0 38 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062455
X-RAY DIFFRACTIONf_angle_d1.2053322
X-RAY DIFFRACTIONf_dihedral_angle_d15.741892
X-RAY DIFFRACTIONf_chiral_restr0.084366
X-RAY DIFFRACTIONf_plane_restr0.005424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.31130.37071440.25582683X-RAY DIFFRACTION88
2.3113-2.64560.32951480.24762614X-RAY DIFFRACTION88
2.6456-3.33260.32731590.22692654X-RAY DIFFRACTION89
3.3326-31.15060.17851360.16492696X-RAY DIFFRACTION89

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