8R8D

Cryo-EM structure of coagulation factor beta-XIIa in complex with the garadacimab Fab fragment (symmetric dimer)

• PDB DOI: https://doi.org/10.2210/pdb8R8D/pdb
• EM Map EMD-18999: EMDB EMDataResource

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-11-29 Released: 2023-12-13 
• Deposition Author(s): Drulyte, I.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for inhibition of beta-FXIIa by garadacimab

Drulyte, I., Ghai, R., Ow, S.Y., Kapp, E.A., Quek, A.J., Panousis, C., Wilson, M.J., Nash, A.D., Pelzing, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 150.95 kDa 
• Atom Count: 7,062 
• Modelled Residue Count: 920 
• Deposited Residue Count: 1,392 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XII	A [auth B], F [auth A]	247	Homo sapiens	Mutation(s): 0  Gene Names: F12
UniProt & NIH Common Fund Data Resources
Find proteins for P00748 (Homo sapiens) Explore P00748  Go to UniProtKB:  P00748
PHAROS:  P00748 GTEx:  ENSG00000131187

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Garadacimab heavy chain variable region	B [auth E], D [auth H]	234	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Garadacimab light chain variable region	C [auth I], E [auth L]	215	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C], H [auth D]	6	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Drulyte, I.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release