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- PDB-9ex9: Cryo EM map and model of the vaccinia minimal RNA polymerase -

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Basic information

Entry
Database: PDB / ID: 9ex9
TitleCryo EM map and model of the vaccinia minimal RNA polymerase
Components(DNA-directed RNA polymerase ...) x 8
KeywordsTRANSCRIPTION / RNA polymerase / RNAP / Vaccinia / MPox / PIC / pre-initiation complex
Function / homology
Function and homology information


viral transcription / DNA-directed RNA polymerase complex / ribonucleoside binding / virion component / : / : / : / : / : / : ...viral transcription / DNA-directed RNA polymerase complex / ribonucleoside binding / virion component / : / : / : / : / : / : / DNA-directed RNA polymerase / host cell cytoplasm / DNA binding / zinc ion binding / metal ion binding
Similarity search - Function
DNA-directed RNA polymerase, 18kDa subunit, poxviral / DNA-directed RNA polymerase, 35kDa subunit, poxviral / RNA polymerase, 22kDa subunit, poxviral / DNA-directed RNA polymerase, 19kDa subunit, poxviral / DNA-directed RNA polymerase, 7kDa polypeptide, chordopoxviral / RNA polymerase, 30kDa subunit, chordopox-type / RNA polymerase, 132kDa subunit, poxvirus-type / RNA polymerase, 30kDa subunit, chordopox-type, N-terminal / Poxvirus DNA-directed RNA polymerase, 18 kD subunit / Poxvirus DNA-directed RNA polymerase, 35 kD subunit ...DNA-directed RNA polymerase, 18kDa subunit, poxviral / DNA-directed RNA polymerase, 35kDa subunit, poxviral / RNA polymerase, 22kDa subunit, poxviral / DNA-directed RNA polymerase, 19kDa subunit, poxviral / DNA-directed RNA polymerase, 7kDa polypeptide, chordopoxviral / RNA polymerase, 30kDa subunit, chordopox-type / RNA polymerase, 132kDa subunit, poxvirus-type / RNA polymerase, 30kDa subunit, chordopox-type, N-terminal / Poxvirus DNA-directed RNA polymerase, 18 kD subunit / Poxvirus DNA-directed RNA polymerase, 35 kD subunit / Poxvirus RNA polymerase 22 kDa subunit / Poxvirus DNA-directed RNA polymerase 19 kDa subunit / Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7) / Poxvirus DNA dependent RNA polymerase 30kDa subunit / Poxvirus DNA dependent RNA polymerase / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, subunit beta-prime / 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, 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, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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
DNA-directed RNA polymerase 147 kDa polypeptide / DNA-directed RNA polymerase 18 kDa subunit / DNA-directed RNA polymerase 30 kDa polypeptide / DNA-directed RNA polymerase 35 kDa subunit / DNA-directed RNA polymerase 7 kDa subunit / DNA-directed RNA polymerase 22 kDa subunit / DNA-directed RNA polymerase 19 kDa subunit / DNA-directed RNA polymerase 133 kDa polypeptide
Similarity search - Component
Biological speciesVaccinia virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsGrimm, C. / Jungwirth, S. / Fischer, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex (CASP target)
Authors: Grimm, C. / Jungwirth, S. / Fischer, U.
History
DepositionApr 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase 147 kDa polypeptide
B: DNA-directed RNA polymerase 133 kDa polypeptide
C: DNA-directed RNA polymerase 35 kDa subunit
E: DNA-directed RNA polymerase 22 kDa subunit
F: DNA-directed RNA polymerase 19 kDa subunit
G: DNA-directed RNA polymerase 18 kDa subunit
J: DNA-directed RNA polymerase 7 kDa subunit
S: DNA-directed RNA polymerase 30 kDa polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)411,94213
Polymers411,6568
Non-polymers2865
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA-directed RNA polymerase ... , 8 types, 8 molecules ABCEFGJS

#1: Protein DNA-directed RNA polymerase 147 kDa polypeptide


Mass: 146995.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: OPG105, RPO147, J6R / Production host: Vaccinia virus / References: UniProt: P20504, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase 133 kDa polypeptide


Mass: 133526.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: OPG151, RPO132, A24R / Production host: Vaccinia virus / References: UniProt: P68694, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase 35 kDa subunit


Mass: 35430.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: OPG156, RPO35, A29L / Production host: Vaccinia virus / References: UniProt: P21087, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase 22 kDa subunit


Mass: 21391.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: OPG103, RPO22, J4R / Production host: Vaccinia virus / References: UniProt: P68608, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase 19 kDa subunit


Mass: 19020.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: OPG131, RPO19, A5R / Production host: Vaccinia virus / References: UniProt: P68610, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase 18 kDa subunit


Mass: 17917.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: OPG119, RPO18, D7R / Production host: Vaccinia virus / References: UniProt: P21034, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase 7 kDa subunit


Mass: 7299.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: OPG090, RPO7, G5.5R / Production host: Vaccinia virus / References: UniProt: P68315, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase 30 kDa polypeptide


Mass: 30074.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: OPG066, RPO30, E4L / Production host: Vaccinia virus / References: UniProt: P21082, DNA-directed RNA polymerase

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Non-polymers , 2 types, 5 molecules

#9: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationY

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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: Vaccinia minimal DNA-directed RNA polymerase / Type: COMPLEX / Entity ID: #1-#3, #5-#8 / Source: NATURAL
Molecular weightValue: 0.55 MDa / Experimental value: YES
Source (natural)Organism: Vaccinia 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: 2200 nm / Nominal defocus min: 1200 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 70 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1particle selection
4cryoSPARC4.1CTF correction
10cryoSPARC4.1initial Euler assignment
13cryoSPARC4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9318600
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 404153 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 92.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004727496
ELECTRON MICROSCOPYf_angle_d0.502137160
ELECTRON MICROSCOPYf_chiral_restr0.04394216
ELECTRON MICROSCOPYf_plane_restr0.00374717
ELECTRON MICROSCOPYf_dihedral_angle_d9.826410366

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