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- PDB-9r78: Human Adenovirus D 10 Capsid Structure -

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Basic information

Entry
Database: PDB / ID: 9r78
TitleHuman Adenovirus D 10 Capsid Structure
Components
  • (Pre-hexon-linking protein ...) x 2
  • Hexon protein
  • Hexon-interlacing protein
  • Penton protein
  • Pre-protein VI
KeywordsVIRUS / adenovirus / capsid / conjunctivitis
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell / host cell cytoplasm ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell / host cell cytoplasm / endocytosis involved in viral entry into host cell / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus Pll, hexon, subdomain 3 / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI ...Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Pre-hexon-linking protein VIII / Adenovirus Pll, hexon, subdomain 3 / Adenovirus hexon associated protein, protein VIII / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Hexon protein / Pre-hexon-linking protein VIII / Hexon-interlacing protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-protein VI
Similarity search - Component
Biological speciesHuman adenovirus D10
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWaraich, 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 support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Biorxiv / Year: 2025
Title: Identification of a novel structural motif and overexpression of key transcripts elucidated in Adenovirus 10
Authors: 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.
History
DepositionMay 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Pre-protein VI
2: Pre-protein VI
3: Pre-protein VI
4: Pre-protein VI
5: Pre-protein VI
6: Pre-protein VI
7: Pre-protein VI
8: Pre-protein VI
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Pre-hexon-linking protein IIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Hexon-interlacing protein


Theoretical massNumber of molelcules
Total (without water)1,704,80728
Polymers1,704,80728
Non-polymers00
Water00
1
1: Pre-protein VI
2: Pre-protein VI
3: Pre-protein VI
4: Pre-protein VI
5: Pre-protein VI
6: Pre-protein VI
7: Pre-protein VI
8: Pre-protein VI
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
M: Penton protein
N: Pre-hexon-linking protein IIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
T: Hexon-interlacing protein
x 60


Theoretical massNumber of molelcules
Total (without water)102,288,4011680
Polymers102,288,4011680
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

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Protein , 4 types, 25 molecules 12345678ABCDEFGHIJKLMQRST

#1: Protein
Pre-protein VI / pVI


Mass: 25546.086 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus D10 / Gene: L3 / Production host: Homo sapiens (human) / References: UniProt: K7ZRR7
#2: Protein
Hexon protein / CP-H / Protein II


Mass: 106268.430 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus D10 / Gene: L3 / Production host: Homo sapiens (human) / References: UniProt: K7ZJY8
#3: Protein Penton protein / CP-P / Penton base protein / Protein III


Mass: 58631.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus D10 / Gene: L2 / Production host: Homo sapiens (human) / References: UniProt: K7ZQ23
#6: Protein
Hexon-interlacing protein / Protein IX


Mass: 13773.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus D10 / Gene: pIX, IX / Production host: Homo sapiens (human) / References: UniProt: K7ZLM2

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Pre-hexon-linking protein ... , 2 types, 3 molecules NOP

#4: Protein Pre-hexon-linking protein IIIa / Capsid vertex-specific component IIIa / CVSC / Protein IIIa / pIIIa


Mass: 62170.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus D10 / Gene: L1 / Production host: Homo sapiens (human) / References: UniProt: K7ZMX4
#5: Protein Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 24660.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus D10 / Gene: L4 / Production host: Homo sapiens (human) / References: UniProt: K7ZJY9

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human adenovirus D10 / Type: VIRUS
Details: Propagation of viral stock in immortalised human cell line and purification by Caesium chloride density gradients.
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Human adenovirus D10
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
Details: Phosphate Buffered Saline (PBS) 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
4CTFFIND4.1.14CTF correction
7Cootmodel fitting
9ISOLDEmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5524 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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