13CM | pdb_000013cm

HAdV-C5 Hexon with coagulation factor II

• PDB DOI: https://doi.org/10.2210/pdb13CM/pdb
• EM Map EMD-76963: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Human adenovirus 5, Homo sapiens
• Mutation(s): No 


• Deposited: 2026-04-29 Released: 2026-07-08 
• Deposition Author(s): Ma, O.X., Reddy, V.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural requirements of blood factors binding to soluble hexon trimers with implications for adenovirus cell targeting and immune evasion

Ma, O.X., Reddy, V.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 332.08 kDa 
• Atom Count: 22,548 
• Modeled Residue Count: 2,809 
• Deposited Residue Count: 2,918 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexon protein	A, B, C	952	Human adenovirus 5	Mutation(s): 0
UniProt
Find proteins for P04133 (Human adenovirus C serotype 5) Explore P04133  Go to UniProtKB:  P04133

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	D [auth G]	62	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	E [auth G], F [auth G], G, H [auth G], I [auth G], J [auth G], K [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU	D [auth G]	L-PEPTIDE LINKING	C6 H9 N O6		GLU

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-08 
Deposition Author(s): Ma, O.X., Reddy, V.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI161367

Revision History  

• Version 1.0: 2026-07-08
  Type: Initial release