5M5Y

RNA Polymerase I elongation complex 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Molecular Structures of Transcribing RNA Polymerase I.

Tafur, L.Sadian, Y.Hoffmann, N.A.Jakobi, A.J.Wetzel, R.Hagen, W.J.Sachse, C.Muller, C.W.

(2016) Mol Cell 64: 1135-1143

  • DOI: 10.1016/j.molcel.2016.11.013
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • RNA polymerase I (Pol I) is a 14-subunit enzyme that solely synthesizes pre-ribosomal RNA. Recently, the crystal structure of apo Pol I gave unprecedented insight into its molecular architecture. Here, we present three cryo-EM structures of elongatin ...

    RNA polymerase I (Pol I) is a 14-subunit enzyme that solely synthesizes pre-ribosomal RNA. Recently, the crystal structure of apo Pol I gave unprecedented insight into its molecular architecture. Here, we present three cryo-EM structures of elongating Pol I, two at 4.0 Å and one at 4.6 Å resolution, and a Pol I open complex at 3.8 Å resolution. Two modules in Pol I mediate the narrowing of the DNA-binding cleft by closing the clamp domain. The DNA is bound by the clamp head and by the protrusion domain, allowing visualization of the upstream and downstream DNA duplexes in one of the elongation complexes. During formation of the Pol I elongation complex, the bridge helix progressively folds, while the A12.2 C-terminal domain is displaced from the active site. Our results reveal the conformational changes associated with elongation complex formation and provide additional insight into the Pol I transcription cycle.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA135B1203Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P22138 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC1C335Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA43G326Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA12I125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC2K142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA49M415Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA34N233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA190A1664Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P10964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA14D137Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P50106 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiaeMutation(s): 0 
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  • Reference Sequence
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Entity ID: 15
MoleculeChainsLengthOrganism
RNAR10Saccharomyces cerevisiae

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Entity ID: 16
MoleculeChainsLengthOrganism
Non-template DNAS70Saccharomyces cerevisiae

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Entity ID: 17
MoleculeChainsLengthOrganism
Template DNAT70Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence, Derived calculations, Experimental preparation
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Other