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- PDB-9zo4: Cryo-EM structure of the complete Pyrococcus furiosus RNA polymer... -

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Basic information

Entry
Database: PDB / ID: 9zo4
TitleCryo-EM structure of the complete Pyrococcus furiosus RNA polymerase in closed clamp conformation
Components(DNA-directed RNA polymerase subunit ...) x 11
KeywordsTRANSCRIPTION / RNA polymerase / Conformations / Promoter loading / Euryarchaea
Function / homology
Function and homology information


tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription elongation by RNA polymerase I / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transcription by RNA polymerase II / protein dimerization activity ...tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription elongation by RNA polymerase I / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transcription by RNA polymerase II / protein dimerization activity / nucleotide binding / magnesium ion binding / DNA-templated transcription / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase, subunit E/RPC8 / HRDC domain superfamily / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 ...DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase, subunit E/RPC8 / HRDC domain superfamily / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / 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, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / 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. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / 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 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / 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 Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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, 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 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo11
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsFordjour, G.N.R. / Armache, J.-P. / Murakami, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM156623 United States
CitationJournal: To Be Published
Title: Clamp conformational flexibility and dynamics in archaeal and eukaryotic RNA polymerases revealed by cryo-EM
Authors: Fordjour, G.N.R. / Murakami, K. / Armache, J.-P. / Murakami, K.S.
History
DepositionDec 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data 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 subunit Rpo1N
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase subunit Rpo1C
D: DNA-directed RNA polymerase subunit Rpo3
E: DNA-directed RNA polymerase subunit Rpo7
F: DNA-directed RNA polymerase subunit Rpo4
H: DNA-directed RNA polymerase subunit Rpo5
K: DNA-directed RNA polymerase subunit Rpo6
L: DNA-directed RNA polymerase subunit Rpo11
N: DNA-directed RNA polymerase subunit Rpo10
P: DNA-directed RNA polymerase subunit Rpo12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,99316
Polymers382,66611
Non-polymers3275
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 subunit ... , 11 types, 11 molecules ABCDEFHKLNP

#1: Protein DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit A'


Mass: 103265.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U0M4, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 127188.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U0M3, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit A''


Mass: 44468.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U0M5, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit D


Mass: 31688.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U0E4, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit E


Mass: 21731.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U439, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit F


Mass: 14116.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U216, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit H


Mass: 9260.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U0M2, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit K


Mass: 6243.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U0E8, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit L


Mass: 11132.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8U4N1, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit N


Mass: 7800.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: P60292, DNA-directed RNA polymerase
#11: Protein/peptide DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit P


Mass: 5770.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: Q8TZI3, DNA-directed RNA polymerase

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Non-polymers , 1 types, 5 molecules

#12: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / 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: RNA polymerase / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#11 / Source: NATURAL
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Buffer solutionpH: 8
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -2200 nm / Nominal defocus min: -800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
7UCSF ChimeraXmodel fitting
9Cootmodel refinement
10PHENIXmodel refinement
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150366 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 107.8 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003426841
ELECTRON MICROSCOPYf_angle_d0.635936237
ELECTRON MICROSCOPYf_chiral_restr0.04664019
ELECTRON MICROSCOPYf_plane_restr0.00514698
ELECTRON MICROSCOPYf_dihedral_angle_d4.39963639

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