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- PDB-9lr9: Local reconstruction of bovine adenovirus type 3 capsid -

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Basic information

Entry
Database: PDB / ID: 9lr9
TitleLocal reconstruction of bovine adenovirus type 3 capsid
Components
  • (Pre-hexon-linking protein ...) x 2
  • Hexon protein
  • PIX
  • PV
  • PVI
  • PX
  • Penton protein
  • Pre-histone-like nucleoprotein
KeywordsVIRAL PROTEIN / Complex
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 / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / virion component / viral penetration into host nucleus / viral capsid / host cell ...hexon binding / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / virion component / viral penetration into host nucleus / viral capsid / host cell / viral nucleocapsid / 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 / DNA binding / membrane
Similarity search - Function
Adenovirus late L2 mu core / Adenovirus late L2 mu core protein (Protein X) / Adenovirus core-capsid bridging protein V / Adenovirus minor core protein PV / Adenoviral core protein VII / Adenoviral core protein VII / Hexon-associated protein IX / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa, N-terminal ...Adenovirus late L2 mu core / Adenovirus late L2 mu core protein (Protein X) / Adenovirus core-capsid bridging protein V / Adenovirus minor core protein PV / Adenoviral core protein VII / Adenoviral core protein VII / 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
Pre-histone-like nucleoprotein / Pre-hexon-linking protein VIII / Penton protein / Pre-hexon-linking protein IIIa / PVI / PV / PX / Hexon protein / PIX
Similarity search - Component
Biological speciesBovine adenovirus 3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsXiao, H. / Liu, H.R.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32371263 China
National Natural Science Foundation of China (NSFC)32401014 China
CitationJournal: J Mol Biol / Year: 2025
Title: Structural Insights into Minor and Core Proteins of Bovine Adenovirus 3: Bridging Capsid and Genomic Core.
Authors: Hao Xiao / Hao Pang / Junquan Zhou / Hao Feng / Jingdong Song / Lingpeng Cheng / Li Wang / Hongrong Liu /
Abstract: Adenoviruses are double-stranded DNA viruses with broad relevance to human and animal health and considerable potential as therapeutic vectors. Despite extensive studies, the structural details of ...Adenoviruses are double-stranded DNA viruses with broad relevance to human and animal health and considerable potential as therapeutic vectors. Despite extensive studies, the structural details of core and minor capsid proteins in adenoviruses remain poorly understood. In this study, the architecture of bovine adenovirus type 3 (BAdV-3), a member of the Mastadenovirus genus, was solved by cryo-electron microscopy. Our structure shows that BAdV-3 shares significant structural conservation with human adenoviruses. Atomic models were constructed for a previously uncharacterized region of the minor protein VI and for the core proteins V and Mu. The study revealed how core proteins bridge the genome and capsid, underscore the multifaceted roles of protein V in strengthening capsid stability and facilitating genome release.
History
DepositionJan 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexon protein
B: PVI
C: Pre-histone-like nucleoprotein
D: Hexon protein
E: PX
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Pre-hexon-linking protein IIIa
L: PVI
M: PV
N: Pre-hexon-linking protein VIII
O: PIX
P: PIX
Q: PIX
R: Pre-hexon-linking protein VIII
S: PVI
T: PVI
U: Pre-histone-like nucleoprotein
V: PIX
X: Hexon protein
Y: Hexon protein
Z: PVI
a: PVI
b: PVI
c: PVI
d: PVI
e: Pre-histone-like nucleoprotein
f: Pre-histone-like nucleoprotein
g: Hexon protein
h: Hexon protein
i: Hexon protein
j: Penton protein


Theoretical massNumber of molelcules
Total (without water)1,842,70735
Polymers1,842,70735
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 7 types, 32 molecules ADFGHIJXYghiBLSTZabcdCUefEMOPQVj

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


Mass: 103148.008 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bovine adenovirus 3 / References: UniProt: P03278
#2: Protein
PVI


Mass: 28249.350 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Bovine adenovirus 3 / References: UniProt: A0A9W3HR60
#3: Protein
Pre-histone-like nucleoprotein / Pre-core protein VII / pVII


Mass: 19002.049 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bovine adenovirus 3 / References: UniProt: A0A9W3HR39
#4: Protein PX / Core protein Mu


Mass: 8514.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bovine adenovirus 3 / References: UniProt: A0A9W3N2I0
#6: Protein PV / Core protein V


Mass: 45388.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bovine adenovirus 3 / References: UniProt: A0A9W3N256
#8: Protein
PIX / Protein IX


Mass: 13719.456 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bovine adenovirus 3 / References: UniProt: Q64845
#9: Protein Penton protein / CP-P / Penton base protein / Protein III


Mass: 55135.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bovine adenovirus 3 / References: UniProt: A0A9W3HR47

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

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


Mass: 63270.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bovine adenovirus 3 / References: UniProt: A0A9W3HR52
#7: Protein Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 23746.486 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bovine adenovirus 3 / References: UniProt: A0A9W3HR45

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Details

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: Bovine adenovirus 3 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bovine adenovirus 3
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45262 / Symmetry type: POINT

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