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

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Basic information

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


3 iron, 4 sulfur cluster binding / 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 ...3 iron, 4 sulfur cluster binding / 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 / metal 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 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
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: 3.37 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

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
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
E: DNA-directed RNA polymerase subunit Rpo7
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 ABCGHKLNYEDPF

#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 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#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
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2-5419_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194130 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 125.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00327862
ELECTRON MICROSCOPYf_angle_d0.54837626
ELECTRON MICROSCOPYf_chiral_restr0.0464289
ELECTRON MICROSCOPYf_plane_restr0.00414823
ELECTRON MICROSCOPYf_dihedral_angle_d4.15193800

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