+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38214 | |||||||||
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Title | The structure of ASFV A137R | |||||||||
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Sample |
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Keywords | dodecahedron / African swine fever virus / polymer / VIRAL PROTEIN | |||||||||
Function / homology | A137R Function and homology information | |||||||||
Biological species | African swine fever virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Li C / Song H / Gao GF | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38214.map.gz | 17.5 MB | EMDB map data format | |
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Header (meta data) | emd-38214-v30.xml emd-38214.xml | 13 KB 13 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38214_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_38214.png | 54.5 KB | ||
Filedesc metadata | emd-38214.cif.gz | 5 KB | ||
Others | emd_38214_half_map_1.map.gz emd_38214_half_map_2.map.gz | 139.7 MB 139.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38214 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38214 | HTTPS FTP |
-Validation report
Summary document | emd_38214_validation.pdf.gz | 575.1 KB | Display | EMDB validaton report |
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Full document | emd_38214_full_validation.pdf.gz | 574.7 KB | Display | |
Data in XML | emd_38214_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | emd_38214_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38214 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38214 | HTTPS FTP |
-Related structure data
Related structure data | 8xb8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_38214.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38214_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38214_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The structure of ASFV A137R
Entire | Name: The structure of ASFV A137R |
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Components |
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-Supramolecule #1: The structure of ASFV A137R
Supramolecule | Name: The structure of ASFV A137R / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: African swine fever virus |
-Macromolecule #1: A137R
Macromolecule | Name: A137R / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: African swine fever virus |
Molecular weight | Theoretical: 16.11455 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MEAVLTKLDQ EEKKALQNFH RCAWEETKNI INDFLEIPEE RCTYKFNSYT KKMELLFTPE FHTAWHEVPE CREFILNFLR LISGHRVVL KGPTFVFTKE IKNLGIPSTI NVDFQANIEN MDDLQKGNLI GKMNIKEG UniProtKB: A137R |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |