9R78 | pdb_00009r78

Human Adenovirus D 10 Capsid Structure

• PDB DOI: https://doi.org/10.2210/pdb9R78/pdb
• EM Map EMD-53736: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Human adenovirus D10
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-05-14 Released: 2025-12-17 
• Deposition Author(s): Waraich, K., Mundy, R.M., Bates, E.A., da Fonseca, P., Morris, E., Rizkallah, P.J., Baker, A.T., Young, M.T., Parker, A.L., Bhella, D.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Identification of a novel structural motif and overexpression of key transcripts elucidated in Adenovirus 10

Mundy, R.M., Waraich, K., Bates, E.A., Rizkallah, P.J., Baker, A.T., Young, M.T., Morris, E., da Fonseca, P.C.A., Bliss, C.M., Matthews, D., Bhella, D., Parker, A.L.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.09.20.677498

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 1680-mer - A720B180C121D120E120F60G60H60I60J60K60L59 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 1680-mer - AA720AB180AC120AD60AE60AF60AG60AH60AI60AJ60AK60AL60AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1BF1BG1BH1BI1BJ1BK1BL1BM1BN1BO1BP1BQ1BR1BS1BT1BU1BV1BW1BX1BY1BZ1Ba1Bb1Bc1Bd1Be1Bf1Bg1Bh1Bi1Bj1Bk1Bl1Bm1Bn1Bo1Bp1Bq1Br1Bs1Bt1Bu1Bv1Bw1Bx1By1Bz1CA1CB1CC1CD1CE1CF1CG1CH1CI1CJ1CK1CL1CM1CN1CO1CP1CQ1CR1CS1CT1CU1CV1CW1CX1CY1CZ1Ca1Cb1 

Local Symmetry: Icosahedral - I  (Explore in 3D)
Local Stoichiometry: Homo 180-mer - B180 Local Symmetry: Icosahedral - I  (Explore in 3D)
Local Stoichiometry: Hetero 360-mer - F60G60H60I60J60K60 Local Symmetry: Icosahedral - I  (Explore in 3D)
Local Stoichiometry: Hetero 1200-mer - A720D120E120H60I60J60K60 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,704.81 kDa 
• Atom Count: 101,221 
• Modeled Residue Count: 12,737 
• Deposited Residue Count: 15,232 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-protein VI	A [auth 1], B [auth 2], C [auth 3], D [auth 4], E [auth 5], F [auth 6], G [auth 7], H [auth 8]	234	Human adenovirus D10	Mutation(s): 0  Gene Names: L3
UniProt
Find proteins for K7ZRR7 (Human adenovirus D10) Explore K7ZRR7  Go to UniProtKB:  K7ZRR7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexon protein	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J], S [auth K], T [auth L]	941	Human adenovirus D10	Mutation(s): 0  Gene Names: L3
UniProt
Find proteins for K7ZJY8 (Human adenovirus D10) Explore K7ZJY8  Go to UniProtKB:  K7ZJY8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Penton protein	U [auth M]	519	Human adenovirus D10	Mutation(s): 0  Gene Names: L2
UniProt
Find proteins for K7ZQ23 (Human adenovirus D10) Explore K7ZQ23  Go to UniProtKB:  K7ZQ23

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-hexon-linking protein IIIa	V [auth N]	559	Human adenovirus D10	Mutation(s): 0  Gene Names: L1
UniProt
Find proteins for K7ZMX4 (Human adenovirus D10) Explore K7ZMX4  Go to UniProtKB:  K7ZMX4

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-hexon-linking protein VIII	W [auth O], X [auth P]	227	Human adenovirus D10	Mutation(s): 0  Gene Names: L4
UniProt
Find proteins for K7ZJY9 (Human adenovirus D10) Explore K7ZJY9  Go to UniProtKB:  K7ZJY9

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexon-interlacing protein	AA [auth S], BA [auth T], Y [auth Q], Z [auth R]	134	Human adenovirus D10	Mutation(s): 0  Gene Names: pIX, IX
UniProt
Find proteins for K7ZLM2 (Human adenovirus D10) Explore K7ZLM2  Go to UniProtKB:  K7ZLM2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	ISOLDE
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Waraich, K., Mundy, R.M., Bates, E.A., da Fonseca, P., Morris, E., Rizkallah, P.J., Baker, A.T., Young, M.T., Parker, A.L., Bhella, D.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release