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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


RNA polymerase III activity / viral transcription / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / virion component / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...RNA polymerase III activity / viral transcription / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / virion component / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / host cell cytoplasm / protein dimerization activity / DNA-templated transcription / DNA binding / zinc ion binding / metal ion binding / cytoplasm
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 / 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. / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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: To Be Published
Title: ASFV RNA polymerase-M1249L complex3
Authors: Feng, X.Y.
History
DepositionMar 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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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

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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