8XY6 | pdb_00008xy6

ASFV RNAP M1249L C-tail occupied complex3 (MCOC3)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Structural basis of RNA polymerase complexes in African swine fever virus.

Zhu, G.Xi, F.Zeng, W.Zhao, Y.Cao, W.Liu, C.Yang, F.Ru, Y.Xiao, S.Zhang, S.Liu, H.Tian, H.Yang, F.Lu, B.Sun, S.Song, H.Sun, B.Zhao, X.Tang, L.Li, K.He, J.Guo, J.Zhu, Y.Zhu, Z.Sun, F.Zheng, H.

(2025) Nat Commun 16: 501-501

  • DOI: https://doi.org/10.1038/s41467-024-55683-z
  • Primary Citation Related Structures: 
    8XX4, 8XX5, 8XXP, 8XXT, 8XY6, 8Y0E

  • PubMed Abstract: 

    African swine fever virus is highly contagious and causes a fatal infectious disease in pigs, resulting in a significant global impact on pork supply. The African swine fever virus RNA polymerase serves as a crucial multifunctional protein complex responsible for genome transcription and regulation. Therefore, it is essential to investigate its structural and functional characteristics for the prevention and control of African swine fever. Here, we determine the structures of endogenous African swine fever virus RNA polymerase in both nucleic acid-free and elongation states. The African swine fever virus RNA polymerase shares similarities with the core of typical RNA polymerases, but possesses a distinct subunit M1249L. Notably, the dynamic binding mode of M1249L with RNA polymerase, along with the C-terminal tail insertion of M1249L in the active center of DNA-RNA scaffold binding, suggests the potential of M1249L to regulate RNA polymerase activity within cells. These results are important for understanding the transcription cycle of the African swine fever virus and for developing antiviral strategies.


  • Organizational Affiliation
    • State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.

Macromolecule Content 

  • Total Structure Weight: 486.68 kDa 
  • Atom Count: 32,407 
  • Modeled Residue Count: 4,059 
  • Deposited Residue Count: 4,282 
  • Unique protein chains: 9

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,441African swine fever virusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P42486 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore P42486 
Go to UniProtKB:  P42486
Entity Groups
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UniProt GroupP42486
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,235African swine fever virusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P42487 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore P42487 
Go to UniProtKB:  P42487
Entity Groups
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UniProt GroupP42487
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase RPB3-11 homolog358African swine fever virusMutation(s): 0 
UniProt
Find proteins for Q65184 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore Q65184 
Go to UniProtKB:  Q65184
Entity Groups
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UniProt GroupQ65184
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase RPB5 homolog205African swine fever virusMutation(s): 0 
UniProt
Find proteins for Q65181 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore Q65181 
Go to UniProtKB:  Q65181
Entity Groups
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UniProt GroupQ65181
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
C147L130African swine fever virusMutation(s): 0 
UniProt
Find proteins for P42484 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore P42484 
Go to UniProtKB:  P42484
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UniProt GroupP42484
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
D339L151African swine fever virusMutation(s): 0 
UniProt
Find proteins for Q89907 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore Q89907 
Go to UniProtKB:  Q89907
Entity Groups
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UniProt GroupQ89907
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
C122R105African swine fever virusMutation(s): 0 
UniProt
Find proteins for Q65157 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore Q65157 
Go to UniProtKB:  Q65157
Entity Groups
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UniProt GroupQ65157
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase RPB10 homolog80African swine fever virusMutation(s): 0 
UniProt
Find proteins for P42488 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore P42488 
Go to UniProtKB:  P42488
Entity Groups
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UniProt GroupP42488
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
M1249L577African swine fever virusMutation(s): 0 
UniProt
Find proteins for Q65152 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore Q65152 
Go to UniProtKB:  Q65152
Entity Groups
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UniProt GroupQ65152
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFD1800100
Ministry of Science and Technology (MoST, China)China2021YFD1801300

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection