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- PDB-8roq: FAdV-C4 Aviadenovirus structure, strain KR5 -

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Basic information

Entry
Database: PDB / ID: 8roq
TitleFAdV-C4 Aviadenovirus structure, strain KR5
Components
  • Hexon protein
  • PIIIa
  • Penton protein
  • Pre-hexon-linking protein VIII
KeywordsVIRUS / adenovirus / fowl / highly thermostable
Function / homology
Function and homology information


hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral capsid / host cell / 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
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 / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Adenovirus Pll, hexon, subdomain 2 / Hexon, adenovirus major coat protein, N-terminal domain ...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 / 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
PIIIa / Penton protein / Hexon protein / Pre-hexon-linking protein VIII
Similarity search - Component
Biological speciesFowl aviadenovirus C
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPerez-Illana, M.P. / Schachnner, A. / Condezo, G.N. / Hernando-Perez, M. / Martinez, M. / Marabini, R. / Hess, M. / San Martin, C.
Funding support2items
OrganizationGrant numberCountry
Other privateLa Caixa Foundation (ID 100010434),La Caixa Foundation (ID 100010434),LCF/BQ/SO16/52270032)
Other governmentco-funded by the Spanish State Research Agency and the European Regional Development Fund, PID2022-136456NB-I00/ AEI/10.13039/501100011033/FEDER,UE
CitationJournal: To Be Published
Title: FAdV-C4 AG234 Aviadenovirus structure, strain KR5
Authors: Perez-Illana, M.P. / Schachnner, A. / Condezo, G.N. / Hernando-Perez, M. / Martinez, M. / Marabini, R. / Hess, M. / San Martin, C.
History
DepositionJan 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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: PIIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII


Theoretical massNumber of molelcules
Total (without water)1,450,09616
Polymers1,450,09616
Non-polymers00
Water00
1
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: PIIIa
O: Pre-hexon-linking protein VIII
P: Pre-hexon-linking protein VIII
x 60


Theoretical massNumber of molelcules
Total (without water)87,005,779960
Polymers87,005,779960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
Hexon protein / CP-H / Protein II


Mass: 106129.789 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Fowl aviadenovirus C / References: UniProt: H8WQV9
#2: Protein Penton protein / CP-P / Penton base protein / Protein III


Mass: 57448.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fowl aviadenovirus C / References: UniProt: F2VJH0
#3: Protein PIIIa / PIIIa protein


Mass: 65326.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fowl aviadenovirus C / References: UniProt: F2VJG9
#4: Protein Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 26882.158 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Fowl aviadenovirus C / References: UniProt: H8WQW6
Has protein modificationN

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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: Fowl aviadenovirus C / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Fowl aviadenovirus C / Strain: KR5
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Gallus gallus
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 95890 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40.5 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9466 / Symmetry type: POINT

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