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- PDB-7ozp: RNA Polymerase II dimer (Class 3) -

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Entry
Database: PDB / ID: 7ozp
TitleRNA Polymerase II dimer (Class 3)
Components
  • (DNA-directed RNA polymerase ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 2
  • (RNA polymerase II subunit ...) x 2
  • RNA_pol_L_2 domain-containing protein
KeywordsTRANSCRIPTION / Polymerase / Dimer / Complex
Function / homology
Function and homology information


: / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway ...: / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / 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 Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / organelle membrane / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / transcription by RNA polymerase III / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / translation initiation factor binding / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / : / : / : / fibrillar center / : / : / : / DNA-directed RNA polymerase / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nuclear speck / nucleotide binding / DNA-templated transcription / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
RNA-binding domain, S1 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 ...RNA-binding domain, S1 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / 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 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / 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. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 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, beta subunit, protrusion / RNA polymerase beta subunit / DNA-directed RNA polymerase, insert domain superfamily / 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 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta / RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase II subunit RPB9
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsAibara, S. / Dienemann, C. / Cramer, P.
Funding support Germany, 5items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission894862 Germany
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
European Research Council (ERC)CHROMATRANS 882357 Germany
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Structure of an inactive RNA polymerase II dimer.
Authors: Shintaro Aibara / Christian Dienemann / Patrick Cramer /
Abstract: Eukaryotic gene transcription is carried out by three RNA polymerases: Pol I, Pol II and Pol III. Although it has long been known that Pol I can form homodimers, it is unclear whether and how the two ...Eukaryotic gene transcription is carried out by three RNA polymerases: Pol I, Pol II and Pol III. Although it has long been known that Pol I can form homodimers, it is unclear whether and how the two other RNA polymerases dimerize. Here we present the cryo-electron microscopy (cryo-EM) structure of a mammalian Pol II dimer at 3.5 Å resolution. The structure differs from the Pol I dimer and reveals that one Pol II copy uses its RPB4-RPB7 stalk to penetrate the active centre cleft of the other copy, and vice versa, giving rise to a molecular handshake. The polymerase clamp domain is displaced and mobile, and the RPB7 oligonucleotide-binding fold mimics the DNA-RNA hybrid that occupies the cleft during active transcription. The Pol II dimer is incompatible with nucleic acid binding as required for transcription and may represent an inactive storage form of the polymerase.
History
DepositionJun 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update
Revision 1.2Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: RNA polymerase II subunit D
E: DNA-directed RNA polymerase II subunit E
F: DNA-directed RNA polymerase II subunit F
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: RNA_pol_L_2 domain-containing protein
L: RNA polymerase II subunit K
M: DNA-directed RNA polymerase subunit
N: DNA-directed RNA polymerase subunit beta
O: DNA-directed RNA polymerase II subunit RPB3
P: RNA polymerase II subunit D
Q: DNA-directed RNA polymerase II subunit E
R: DNA-directed RNA polymerase II subunit F
S: DNA-directed RNA polymerase II subunit RPB7
T: DNA-directed RNA polymerases I, II, and III subunit RPABC3
U: DNA-directed RNA polymerase II subunit RPB9
V: DNA-directed RNA polymerases I, II, and III subunit RPABC5
W: RNA_pol_L_2 domain-containing protein
X: RNA polymerase II subunit K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,035,42334
Polymers1,034,76924
Non-polymers65410
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area109240 Å2
ΔGint-563 kcal/mol
Surface area255780 Å2

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Components

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DNA-directed RNA polymerase ... , 7 types, 14 molecules AMBNCOEQFRGSIU

#1: Protein DNA-directed RNA polymerase subunit


Mass: 217450.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 134041.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig)
References: UniProt: A0A0B8RVL1, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3


Mass: 31439.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A481DF93
#5: Protein DNA-directed RNA polymerase II subunit E / RPB5 homolog


Mass: 24644.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LSI7
#6: Protein DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I / II / and III subunit RPABC2 / RPB6 homolog


Mass: 14477.001 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: F1SKN8
#7: Protein DNA-directed RNA polymerase II subunit RPB7


Mass: 19314.283 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LJZ9
#9: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 kDa subunit / RPB14.5


Mass: 14541.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: P60899

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RNA polymerase II subunit ... , 2 types, 4 molecules DPLX

#4: Protein RNA polymerase II subunit D


Mass: 16331.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A287ADR4
#12: Protein RNA polymerase II subunit K


Mass: 7018.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LN51

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DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 4 molecules HTJV

#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 17162.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A4X1ULF2
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5


Mass: 7655.123 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A7K6NXI9

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Protein / Non-polymers , 2 types, 12 molecules KW

#11: Protein RNA_pol_L_2 domain-containing protein


Mass: 13310.284 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A4X1UK25
#13: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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 II dimer / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Molecular weightValue: 1.1 MDa / Experimental value: NO
Source (natural)Organism: Sus scrofa domesticus (domestic pig)
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: 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
Image recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41379 / Symmetry type: POINT

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