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- PDB-7aoe: Schizosaccharomyces pombe RNA polymerase I (elongation complex) -

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Entry
Database: PDB / ID: 7aoe
TitleSchizosaccharomyces pombe RNA polymerase I (elongation complex)
Components
  • (DNA-directed RNA polymerase I subunit ...) x 4
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • Probable DNA-directed RNA polymerase I subunit RPA2
  • RNA
  • non-template DNA
  • template DNA
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / RNA polymerase II, holoenzyme / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter ...RNA Polymerase I Transcription Initiation / RNA polymerase II, holoenzyme / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / mRNA Splicing - Major Pathway / Transcriptional regulation by small RNAs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA-templated transcription elongation / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase III / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / DNA-directed RNA polymerase activity / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleolus / mitochondrion / DNA binding / zinc ion binding / metal ion binding / nucleus / cytosol
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1060 / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / RNA polymerase Rpb7-like, N-terminal domain / Pol I subunit A12, C-terminal zinc ribbon / RPA43, OB domain / RPA43 OB domain in RNA Pol I / DNA-directed RNA polymerase I subunit RPA2, domain 4 / DNA-directed RNA pol I, largest subunit / : ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1060 / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / RNA polymerase Rpb7-like, N-terminal domain / Pol I subunit A12, C-terminal zinc ribbon / RPA43, OB domain / RPA43 OB domain in RNA Pol I / DNA-directed RNA polymerase I subunit RPA2, domain 4 / DNA-directed RNA pol I, largest subunit / : / RNA polymerase I, Rpa2 specific domain / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Zinc finger TFIIS-type signature. / 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 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / 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, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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. / Dna Ligase; domain 1 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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, 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 / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase I subunit rpa43 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerase I subunit rpa1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 ...DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase I subunit rpa43 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerase I subunit rpa1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase I subunit rpa14 / Probable DNA-directed RNA polymerase I subunit RPA2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHeiss, F. / Daiss, J. / Becker, P. / Engel, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 960 (TP-A8) Germany
German Research Foundation (DFG)EN 1204/1-1 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Conserved strategies of RNA polymerase I hibernation and activation.
Authors: Florian B Heiss / Julia L Daiß / Philipp Becker / Christoph Engel /
Abstract: RNA polymerase (Pol) I transcribes the ribosomal RNA precursor in all eukaryotes. The mechanisms 'activation by cleft contraction' and 'hibernation by dimerization' are unique to the regulation of ...RNA polymerase (Pol) I transcribes the ribosomal RNA precursor in all eukaryotes. The mechanisms 'activation by cleft contraction' and 'hibernation by dimerization' are unique to the regulation of this enzyme, but structure-function analysis is limited to baker's yeast. To understand whether regulation by such strategies is specific to this model organism or conserved among species, we solve three cryo-EM structures of Pol I from Schizosaccharomyces pombe in different functional states. Comparative analysis of structural models derived from high-resolution reconstructions shows that activation is accomplished by a conserved contraction of the active center cleft. In contrast to current beliefs, we find that dimerization of the S. pombe polymerase is also possible. This dimerization is achieved independent of the 'connector' domain but relies on two previously undescribed interfaces. Our analyses highlight the divergent nature of Pol I transcription systems from their counterparts and suggest conservation of regulatory mechanisms among organisms.
History
DepositionOct 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase I subunit rpa1
B: Probable DNA-directed RNA polymerase I subunit RPA2
C: DNA-directed RNA polymerases I and III subunit RPAC1
D: DNA-directed RNA polymerase I subunit rpa14
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase I subunit rpa43
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase I subunit RPA12
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerases I and III subunit RPAC2
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
U: non-template DNA
T: template DNA
R: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)524,15021
Polymers523,75715
Non-polymers3926
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area64260 Å2
ΔGint-334 kcal/mol
Surface area156060 Å2
MethodPISA

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Components

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DNA-directed RNA polymerase I subunit ... , 4 types, 4 molecules ADGI

#1: Protein DNA-directed RNA polymerase I subunit rpa1 / DNA-directed RNA polymerase I 190 kDa polypeptide / DNA-directed RNA polymerase I largest subunit


Mass: 189489.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / References: UniProt: P15398, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase I subunit rpa14 / RNA polymerase I subunit A14 / DNA-directed RNA polymerase I 17 kDa polypeptide / Nucleolar protein ker1


Mass: 17008.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / References: UniProt: Q9P7P1
#7: Protein DNA-directed RNA polymerase I subunit rpa43 / RNA polymerase I subunit A43 / DNA-dependent RNA polymerase 19 kDa polypeptide


Mass: 19406.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / References: UniProt: O43036
#9: Protein DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerase I 13.1 kDa polypeptide


Mass: 13127.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / References: UniProt: O94703

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DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK

#3: Protein DNA-directed RNA polymerases I and III subunit RPAC1 / RNA polymerases I and III subunit AC1 / DNA-directed RNA polymerases I and III 40 kDa polypeptide / ...RNA polymerases I and III subunit AC1 / DNA-directed RNA polymerases I and III 40 kDa polypeptide / AC40 / RPC39


Mass: 39205.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / References: UniProt: O94616
#11: Protein DNA-directed RNA polymerases I and III subunit RPAC2 / RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerases I and III 14 kDa polypeptide


Mass: 13734.478 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: rpc19, rpa17, SPAC1687.01, SPAPYUL23.01 / Production host: Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09177

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / RPC24B


Mass: 23954.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / References: UniProt: Q09191
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / and III 15 kDa ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / and III 15 kDa polypeptide / RPC16


Mass: 15742.497 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / References: UniProt: P36595
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / and III 14.5 kDa ...RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide / RPC14


Mass: 14317.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / References: UniProt: Q92399
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / DNA-directed RNA polymerases I / and ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide / RPC8


Mass: 8286.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / References: UniProt: O13877
#12: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7216.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / References: UniProt: P48011

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DNA chain , 2 types, 2 molecules UT

#13: DNA chain non-template DNA


Mass: 12085.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#14: DNA chain template DNA


Mass: 11942.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / RNA chain / Non-polymers , 3 types, 8 molecules BR

#15: RNA chain RNA


Mass: 6383.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#2: Protein Probable DNA-directed RNA polymerase I subunit RPA2 / DNA-directed RNA polymerase I polypeptide 2 / RNA polymerase I subunit 2


Mass: 131854.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / References: UniProt: Q9P7X8, DNA-directed RNA polymerase

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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

Component
IDNameTypeEntity IDParent-IDSource
1S. pombe RNA polymerase I - elongation complexCOMPLEX#1-#150MULTIPLE SOURCES
2S. pombe RNA polymerase I - elongation complexCOMPLEX#1-#10, #121NATURAL
3DNA-directed RNA polymerases I and III subunit RPAC2COMPLEX#111RECOMBINANT
4DNA, RNACOMPLEX#13-#151RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)284812
33Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)284812
44synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Schizosaccharomyces pombe (fission yeast)4896
24synthetic construct (others)32630
Buffer solutionpH: 7.8
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 88.28 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61954 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 48.46 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007431540
ELECTRON MICROSCOPYf_angle_d0.845242818
ELECTRON MICROSCOPYf_chiral_restr0.04844788
ELECTRON MICROSCOPYf_plane_restr0.00555347
ELECTRON MICROSCOPYf_dihedral_angle_d17.98064564

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