Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 215.05 kDa 
• Atom Count: 13,287 
• Modelled Residue Count: 1,665 
• Deposited Residue Count: 1,893 
• Unique protein chains: 3

 8G6I

Coagulation factor VIII bound to a patient-derived anti-C1 domain antibody inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb8G6I/pdb
• EM Map EMD-29770: EMDB EMDataResource

• Classification: BLOOD CLOTTING
• Organism(s): Sus scrofa, Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2023-02-15 Released: 2023-05-24 
• Deposition Author(s): Childers, K.C., Davulcu, O., Haynes, R.M., Lollar, P., Doering, C.B., Coxon, C.H., Spiegel, P.C.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of coagulation factor VIII bound to a patient-derived anti-C1 domain antibody inhibitor.

Childers, K.C., Avery, N.G., Estrada Alamo, K.A., Davulcu, O., Haynes, R.M., Lollar, P., Doering, C.B., Coxon, C.H., Spiegel, P.C.

(2023) Blood 

• PubMed: 37192299 
• DOI: https://doi.org/10.1182/blood.2023020181
• Primary Citation of Related Structures:  
  8G6I


• PubMed Abstract: 
  

The development of pathogenic antibody inhibitors against coagulation factor VIII (FVIII) occurs in approximately 30% of congenital hemophilia A patients receiving FVIII replacement therapy as well as in all cases of acquired hemophilia A. KM33 is an anti-C1 domain antibody inhibitor previously isolated from a severe hemophilia A patient. In addition to potently blocking FVIII binding to von Willebrand factor and phospholipid surfaces, KM33 disrupts FVIII binding to lipoprotein receptor-related protein 1 (LRP1), which drives FVIII hepatic clearance and antigen presentation in dendritic cells. Here, we report on the structure of FVIII bound to NB33, a recombinant derivative of KM33, by single-particle cryo-electron microscopy. Structural analysis reveals the NB33 epitope localizes to FVIII residues R2090-S2094 and I2158-R2159 which constitute membrane-binding loops in the C1 domain. Further analysis reveals multiple FVIII lysine and arginine residues, previously shown to mediate binding to LRP1, dock onto an acidic cleft at the NB33 variable domain interface, thus blocking a putative LRP1 binding site. Together, these results demonstrate a novel mechanism of FVIII inhibition by a patient-derived antibody inhibitor and provide structural evidence toward engineering FVIII with reduced LRP1-mediated clearance.

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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 chimera from human and pig	A	1,467	Sus scrofa, Homo sapiens	Mutation(s): 0  Gene Names: F8, CF8, F8C
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
UniProt Groups	P12263P00451

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NB33 light chain	B	211	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NB33 heavy chain	C	215	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2
MODEL REFINEMENT	PHENIX	1.20

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Childers, K.C., Davulcu, O., Haynes, R.M., Lollar, P., Doering, C.B., Coxon, C.H., Spiegel, P.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R15HL135658
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 Institute of General Medical Sciences (NIH/NIGMS)	United States	U24GM129547

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release