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- PDB-8yqw: ASFV RNA polymerase-M1249L complex3 -

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Basic information

Entry
Database: PDB / ID: 8yqw
TitleASFV RNA polymerase-M1249L complex3
Components
  • (DNA-directed RNA polymerase ...) x 5
  • C122R
  • C147L
  • D339L
  • M1249L
KeywordsVIRAL PROTEIN / ASFV / RNAP
Function / homology
Function and homology information


viral transcription / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / DNA-directed RNA polymerase complex / virion component / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transcription by RNA polymerase II ...viral transcription / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / DNA-directed RNA polymerase complex / virion component / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transcription by RNA polymerase II / host cell cytoplasm / protein dimerization activity / DNA-templated transcription / DNA binding / zinc ion binding
Similarity search - Function
RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. ...RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6
Similarity search - Domain/homology
C122R / DNA-directed RNA polymerase RPB5 homolog / DNA-directed RNA polymerase RPB10 homolog / C147L / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase RPB3-11 homolog / D339L / M1249L / DNA-directed RNA polymerase subunit
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsFeng, X.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Transcription regulation of African swine fever virus: dual role of M1249L.
Authors: Dongming Zhao / Nan Wang / Xiaoying Feng / Zhenjiang Zhang / Kongen Xu / Tao Zheng / Yunge Yang / Xuemei Li / Xianjin Ou / Rui Zhao / Zihe Rao / Zhigao Bu / Yutao Chen / Xiangxi Wang /
Abstract: African swine fever virus (ASFV), which poses significant risks to the global economy, encodes a unique host-independent transcription system. This system comprises an eight-subunit RNA polymerase ...African swine fever virus (ASFV), which poses significant risks to the global economy, encodes a unique host-independent transcription system. This system comprises an eight-subunit RNA polymerase (vRNAP), temporally expressed transcription factors and transcript associated proteins, facilitating cross-species transmission via intermediate host. The protein composition of the virion and the presence of transcription factors in virus genome suggest existence of distinct transcription systems during viral infection. However, the precise mechanisms of transcription regulation remain elusive. Through analyses of dynamic transcriptome, vRNAP-associated components and cell-based assay, the critical role of M1249L in viral transcription regulation has been highlighted. Atomic-resolution structures of vRNAP-M1249L supercomplex, exhibiting a variety of conformations, have uncovered the dual functions of M1249L. During early transcription, M1249L could serve as multiple temporary transcription factors with C-terminal domain acting as a switcher for activation/inactivation, while during late transcription it aids in the packaging of the transcription machinery. The structural and functional characteristics of M1249L underscore its vital roles in ASFV transcription, packaging, and capsid assembly, presenting novel opportunities for therapeutic intervention.
History
DepositionMar 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
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Revision 1.1Jun 11, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
E: C147L
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase RPB3-11 homolog
D: DNA-directed RNA polymerase RPB5 homolog
H: DNA-directed RNA polymerase RPB10 homolog
G: C122R
J: M1249L
F: D339L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)590,66119
Polymers590,0489
Non-polymers61310
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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DNA-directed RNA polymerase ... , 5 types, 5 molecules ABCDH

#1: Protein DNA-directed RNA polymerase subunit / vRPB1


Mass: 163933.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus
References: UniProt: A0A3S7XUW7, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta / vRPB2


Mass: 140056.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus
References: UniProt: A0A2X0RU95, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase RPB3-11 homolog / vRPB3-11


Mass: 41418.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A2X0RUE7
#5: Protein DNA-directed RNA polymerase RPB5 homolog / vRPB5


Mass: 23693.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A0A1E0C1
#6: Protein DNA-directed RNA polymerase RPB10 homolog / vRPB10


Mass: 9040.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A0C5BCR6

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Protein , 4 types, 4 molecules EGJF

#2: Protein C147L / vRPB6 / C147L protein / Protein C147L


Mass: 16670.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A2X0RTW5
#7: Protein C122R / vRPB9 / C122R protein / PC105R / PC122R


Mass: 11831.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A0A1DYD1
#8: Protein M1249L / M1249L protein / Protein M1249L


Mass: 144604.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A2X0SDX8
#9: Protein D339L / vRPB7 / D339L protein / Protein D339L


Mass: 38798.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) African swine fever virus / References: UniProt: A0A2X0RV08

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Non-polymers , 2 types, 10 molecules

#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#11: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
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: ASFV RNA polymerase-M1249L complex3 / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Source (natural)Organism: African swine fever virus
Buffer solutionpH: 7.5
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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 218831 / Symmetry type: POINT

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