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- PDB-8xb8: The structure of ASFV A137R -

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Basic information

Entry
Database: PDB / ID: 8xb8
TitleThe structure of ASFV A137R
ComponentsA137R
KeywordsVIRAL PROTEIN / dodecahedron / African swine fever virus / polymer
Function / homologyA137R
Function and homology information
Biological speciesAfrican swine fever virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi, C. / Song, H. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Virol / Year: 2024
Title: African swine fever virus A137R assembles into a dodecahedron cage.
Authors: Changyao Li / Mingzhu Jia / Tianjiao Hao / Qi Peng / Ruchao Peng / Yan Chai / Yi Shi / Hao Song / George F Gao /
Abstract: African swine fever (ASF) is a highly contagious viral disease that affects domestic and wild pigs. The causative agent of ASF is African swine fever virus (ASFV), a large double-stranded DNA virus ...African swine fever (ASF) is a highly contagious viral disease that affects domestic and wild pigs. The causative agent of ASF is African swine fever virus (ASFV), a large double-stranded DNA virus with a complex virion structure. Among the various proteins encoded by ASFV, A137R is a crucial structural protein associated with its virulence. However, the structure and molecular mechanisms underlying the functions of A137R remain largely unknown. In this study, we present the structure of A137R determined by cryogenic electron microscopy single-particle reconstruction, which reveals that A137R self-oligomerizes to form a dodecahedron-shaped cage composed of 60 polymers. The dodecahedron is literally equivalent to a 1 icosahedron where the icosahedral vertexes are located in the center of each dodecahedral facet. Within each facet, five A137R protomers are arranged in a head-to-tail orientation with a long N-terminal helix forming the edge through which adjacent facets stitch together to form the dodecahedral cage. Combining structural analysis and biochemical evidence, we demonstrate that the N-terminal domain of A137R is crucial and sufficient for mediating the assembly of the dodecahedron. These findings imply the role of A137R cage as a core component in the icosahedral ASFV virion and suggest a promising molecular scaffold for nanotechnology applications.
IMPORTANCE: African swine fever (ASF) is a lethal viral disease of pigs caused by African swine fever virus (ASFV). No commercial vaccines and antiviral treatments are available for the prevention ...IMPORTANCE: African swine fever (ASF) is a lethal viral disease of pigs caused by African swine fever virus (ASFV). No commercial vaccines and antiviral treatments are available for the prevention and control of the disease. A137R is a structural protein of ASFV that is associated with its virulence. The discovery of the dodecahedron-shaped cage structure of A137R in this study is of great importance in understanding ASFV pathogenicity. This finding sheds light on the molecular mechanisms underlying the functions of A137R. Furthermore, the dodecahedral cage formed by A137R shows promise as a molecular scaffold for nanoparticle vectors. Overall, this study provides valuable insights into the structure and function of A137R, contributing to our understanding of ASFV and potentially opening up new avenues for the development of vaccines or treatments for ASF.
History
DepositionDec 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A137R
B: A137R
C: A137R
D: A137R
E: A137R
F: A137R
G: A137R
H: A137R
I: A137R
J: A137R
K: A137R
L: A137R
M: A137R
N: A137R
O: A137R
P: A137R
Q: A137R
R: A137R
S: A137R
T: A137R
U: A137R
V: A137R
W: A137R
X: A137R
Y: A137R
Z: A137R
a: A137R
b: A137R
c: A137R
d: A137R
e: A137R
f: A137R
g: A137R
h: A137R
i: A137R
j: A137R
k: A137R
l: A137R
m: A137R
n: A137R
o: A137R
p: A137R
q: A137R
r: A137R
s: A137R
t: A137R
u: A137R
v: A137R
w: A137R
x: A137R
y: A137R
z: A137R
0: A137R
1: A137R
2: A137R
3: A137R
4: A137R
5: A137R
6: A137R
7: A137R


Theoretical massNumber of molelcules
Total (without water)966,87360
Polymers966,87360
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area151250 Å2
ΔGint-1331 kcal/mol
Surface area269340 Å2

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Components

#1: Protein ...
A137R / ASFV A137R


Mass: 16114.550 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: A137R CDS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2X0THQ0

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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: The structure of ASFV A137R / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: African swine fever virus
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130876 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00351720
ELECTRON MICROSCOPYf_angle_d0.569720
ELECTRON MICROSCOPYf_dihedral_angle_d16.10119380
ELECTRON MICROSCOPYf_chiral_restr0.0457500
ELECTRON MICROSCOPYf_plane_restr0.0038820

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