Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 217.29 kDa 
• Atom Count: 13606 
• Modelled Residue Count: 1695 
• Deposited Residue Count: 1903 
• Unique protein chains: 3

7K66

Structure of Blood Coagulation Factor VIII in Complex with an Anti-C1 Domain Pathogenic Antibody Inhibitor

• PDB DOI: 10.2210/pdb7K66/pdb

• Classification: BLOOD CLOTTING/Immune System
• Organism(s): Sus scrofa, Homo sapiens, Mus musculus
• Expression System: Cricetulus griseus, Mus musculus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2020-09-18 Released: 2020-10-14 
• Deposition Author(s): Childers, K.C., Gish, J., Jarvis, L., Peters, S., Garrels, C., Smith, I.W., Spencer, H.T., Spiegel, P.C.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.92 Å
• R-Value Free: 0.322 
• R-Value Work: 0.226 
• R-Value Observed: 0.234 

Literature

Structure of blood coagulation factor VIII in complex with an anti-C1 domain pathogenic antibody inhibitor.

Gish, J.S., Jarvis, L., Childers, K.C., Peters, S.C., Garrels, C.S., Smith, I.W., Spencer, H.T., Doering, C.B., Lollar, P., Spiegel, P.C.

(2021) Blood 137: 2981-2986

• PubMed: 33529335 
• DOI: 10.1182/blood.2020008940
• Primary Citation of Related Structures:  
  7K66


• PubMed Abstract: 
  

Antibody inhibitor development in hemophilia A represents the most significant complication resulting from factor VIII (fVIII) replacement therapy. Recent studies have demonstrated that epitopes present in the C1 domain contribute to a pathogenic inhibitor response. In this study, we report the structure of a Group A anti-C1 domain inhibitor, termed 2A9, in complex with a B domain-deleted, bioengineered fVIII construct (ET3i). The 2A9 epitope forms direct contacts to the C1 domain at three different surface loops consisting of Lys2065-Trp2070, Arg2150-Tyr2156 and Lys2110-Trp2112. Additional contacts are observed between 2A9 and the A3 domain, including the Phe1743-Tyr1748 loop and the N-linked glycosylation at Asn1810. Most of the C1 domain loops in the 2A9 epitope also represent a putative interface between fVIII and von Willebrand factor (vWF). Lastly, the C2 domain in the ET3i:2A9 complex adopts a large, novel conformational change, translocating outward from the structure of fVIII by 20 Å. This study reports the first structure of an anti-C1 domain antibody inhibitor and the first fVIII:inhibitor complex with a therapeutically active fVIII construct. Further structural understanding of fVIII immunogenicity may result in the development of more effective and safe fVIII replacement therapies.

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Organizational Affiliation: 

Western Washington University, Bellingham, Washington, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII	A	1467	Sus scrofa, Homo sapiens	Mutation(s): 0  Gene Names: F8, CF8, F8C Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P12263 (Sus scrofa) Explore P12263  Go to UniProtKB:  P12263
Find proteins for P00451 (Homo sapiens) Explore P00451  Go to UniProtKB:  P00451
PHAROS:  P00451 GTEx:  ENSG00000185010
UniProt Groups	P00451P12263

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2A9 heavy chain	B	223	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
2A9 light chain	C	213	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth H]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth D]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	G [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.92 Å
• R-Value Free: 0.322 
• R-Value Work: 0.226 
• R-Value Observed: 0.234 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.721	α = 90
b = 116.721	β = 90
c = 371.057	γ = 90

Software Package:

Software Name	Purpose
Adxv	data reduction
XDS	data reduction
PHASER	phasing
Coot	model building
PHENIX	refinement
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-09-18 
• Released Date: 2020-10-14 
Deposition Author(s): Childers, K.C., Gish, J., Jarvis, L., Peters, S., Garrels, C., Smith, I.W., Spencer, H.T., Spiegel, P.C.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MRI 1429164
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R15HL103518
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	U54HL141981
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R44HL117511
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R44HL110448
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	U54HL112309

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2021-02-24
  Changes: Database references
• Version 1.2: 2021-06-09
  Changes: Database references