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- PDB-9zoh: Cryo-EM structure of the complete Sulfolobus acidocaldarius RNA p... -

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Basic information

Entry
Database: PDB / ID: 9zoh
TitleCryo-EM structure of the complete Sulfolobus acidocaldarius RNA polymerase in open clamp conformation
Components(DNA-directed RNA polymerase subunit ...) x 13
KeywordsTRANSCRIPTION / RNA polymerase / Conformations / Promoter loading / Crenarchaea
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / iron-sulfur cluster binding / DNA-templated transcription initiation / transcription by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity ...DNA-directed RNA polymerase complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / iron-sulfur cluster binding / DNA-templated transcription initiation / transcription by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / nucleotide binding / magnesium ion binding / DNA-templated transcription / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / 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 ...RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / 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 Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / 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 Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, funnel domain superfamily / 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
IRON/SULFUR CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo11 ...IRON/SULFUR CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo13 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo4
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 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: J Biol Chem / Year: 2026
Title: Clamp conformational flexibility and dynamics in archaeal and eukaryotic RNA polymerases revealed by cryo-EM.
Authors: George N R Fordjour / Leon Palao / Kenji Murakami / Jean-Paul Armache / Katsuhiko S Murakami /
Abstract: All cellular RNA polymerases (RNAPs) across Bacteria, Archaea, and Eukarya share a conserved catalytic core, yet bacterial and archaeal-eukaryotic RNAPs diverged after separation from the last ...All cellular RNA polymerases (RNAPs) across Bacteria, Archaea, and Eukarya share a conserved catalytic core, yet bacterial and archaeal-eukaryotic RNAPs diverged after separation from the last universal common ancestor. This evolutionary split produced distinct subunit compositions and fundamentally different requirements for external factors during transcription initiation. Bacterial RNAP relies on a σ factor, whereas archaeal-eukaryotic RNAPs require a more extensive set of general transcription factors (GTFs) to bind promoter DNA, unwind the duplex, and position the template strand within the active site cleft. Notably, despite the close structural similarity between archaeal and eukaryotic RNAPs, the requirement for GTFs became further specialized after the emergence of Eukarya. This divergence raises the question of whether differences in intrinsic conformational flexibility and dynamics of these RNAPs contribute to distinct promoter-loading pathways. In this study, we addressed this question using cryo-electron microscopy (cryo-EM) to examine archaeal RNAPs from Euryarchaeota and Crenarchaeota alongside yeast RNAP II. Archaeal RNAP displays a highly dynamic DNA binding clamp domain that samples a broad spectrum of open and closed states, whereas RNAP II predominantly adopts a closed clamp state. Both archaeal and eukaryotic RNAPs can be found in stalk-bound and stalk-less forms. Comparative structural analyses further reveal a unique conformational transition in crenarchaeal RNAP associated with clamp opening. Together, these findings define the intrinsic clamp-conformational landscapes across the archaeal-eukaryotic lineage and suggest that evolutionary tuning of clamp flexibility and dynamics contributes to distinct GTF-dependent promoter-loading mechanisms.
History
DepositionDec 15, 2025Deposition site: RCSB / Processing site: RCSB
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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 Rpo1N
B: DNA-directed RNA polymerase subunit Rpo2
C: DNA-directed RNA polymerase subunit Rpo1C
E: DNA-directed RNA polymerase subunit Rpo7
G: DNA-directed RNA polymerase subunit Rpo8
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
Y: DNA-directed RNA polymerase subunit Rpo13
D: DNA-directed RNA polymerase subunit Rpo3
P: DNA-directed RNA polymerase subunit Rpo12
F: DNA-directed RNA polymerase subunit Rpo4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)405,11119
Polymers404,43213
Non-polymers6796
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 ... , 13 types, 13 molecules ABCEGHKLNYDPF

#1: Protein DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit A / DNA-directed RNA polymerase subunit A' / Rpo1'


Mass: 99929.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P11512, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit B


Mass: 126647.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P11513, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit A'' / DNA-directed RNA polymerase subunit C / Rpo1''


Mass: 44507.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P11514, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit E


Mass: 20496.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39466, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase / subunit G


Mass: 14463.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAY4, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit H


Mass: 9477.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P11521, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit K


Mass: 10251.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39463, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit L


Mass: 10061.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P46217, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit N


Mass: 7673.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39472, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase subunit Rpo13 / DNA-directed RNA polymerase subunit F


Mass: 12331.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAJ6, DNA-directed RNA polymerase
#11: Protein DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit D


Mass: 29858.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39471, DNA-directed RNA polymerase
#12: Protein/peptide DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit P


Mass: 5662.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAE8, DNA-directed RNA polymerase
#13: Protein DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit F


Mass: 13070.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB12, DNA-directed RNA polymerase

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Non-polymers , 2 types, 6 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has ligand of interestN
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: RNA polymerase / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#13 / Source: NATURAL
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
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: -2400 nm / Nominal defocus min: -1000 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
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81025 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 118.68 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004627737
ELECTRON MICROSCOPYf_angle_d0.654937455
ELECTRON MICROSCOPYf_chiral_restr0.04854268
ELECTRON MICROSCOPYf_plane_restr0.00514801
ELECTRON MICROSCOPYf_dihedral_angle_d4.7423782

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