6RUO

RNA Polymerase I Open Complex conformation 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular insight into RNA polymerase I promoter recognition and promoter melting.

Sadian, Y.Baudin, F.Tafur, L.Murciano, B.Wetzel, R.Weis, F.Muller, C.W.

(2019) Nat Commun 10: 5543-5543

  • DOI: 10.1038/s41467-019-13510-w
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • RNA polymerase I (Pol I) assembles with core factor (CF) and Rrn3 on the rDNA core promoter for transcription initiation. Here, we report cryo-EM structures of closed, intermediate and open Pol I initiation complexes from 2.7 to 3.7 Å resolution to v ...

    RNA polymerase I (Pol I) assembles with core factor (CF) and Rrn3 on the rDNA core promoter for transcription initiation. Here, we report cryo-EM structures of closed, intermediate and open Pol I initiation complexes from 2.7 to 3.7 Å resolution to visualize Pol I promoter melting and to structurally and biochemically characterize the recognition mechanism of Pol I promoter DNA. In the closed complex, double-stranded DNA runs outside the DNA-binding cleft. Rotation of CF and upstream DNA with respect to Pol I and Rrn3 results in the spontaneous loading and opening of the promoter followed by cleft closure and positioning of the Pol I A49 tandem winged helix domain (tWH) onto DNA. Conformational rearrangement of A49 tWH leads to a clash with Rrn3 to initiate complex disassembly and promoter escape. Comprehensive insight into the Pol I transcription initiation cycle allows comparisons with promoter opening by Pol II and Pol III.


    Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany. cmueller@embl.de.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA49M415Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPA49RRN13YNL248CN0880
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA135B1203Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPA135RPA2RRN2SRP3YPR010CYP9531.03C
EC: 2.7.7.6
Find proteins for P22138 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC1C335Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPC40RPA5RPC5YPR110CP8283.18
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA14D137Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPA14YDR156WYD8358.11
Find proteins for P50106 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA43G326Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPA43RRN12YOR340CO6271
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPB10YOR210W
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN7Q514Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRN7YJL025WJ1273
Find proteins for P40992 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA12I125Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPA12RRN4YJR063WJ1747
Find proteins for P32529 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC2K142Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPC19YNL113WN1937
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA34N233Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPA34YJL148WJ0637
Find proteins for P47006 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN3O627Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRN3YKL125W
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN6S894Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRN6YBL014CYBL0311YBL0312
Find proteins for P32786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN11R507Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RRN11YML043CYM9827.09C
Find proteins for Q04712 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA190A1664Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPA190RPA1RRN1YOR341WO6276
EC: 2.7.7.6
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPB5RPA7RPC9YBR154CYBR1204
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
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  • Reference Sequence

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Entity ID: 19
MoleculeChainsLengthOrganism
Template strandT70synthetic construct

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Entity ID: 20
MoleculeChainsLengthOrganism
Nontemplate strandU70synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, I, J, L, Q
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilERC-2013-AdG340964-POL1PIC

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references