5LMX

Monomeric RNA polymerase I at 4.9 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription.

Torreira, E.Louro, J.A.Pazos, I.Gonzalez-Polo, N.Gil-Carton, D.Duran, A.G.Tosi, S.Gallego, O.Calvo, O.Fernandez-Tornero, C.

(2017) Elife 6

  • DOI: 10.7554/eLife.20832
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental process must be precisely regulated to satisfy cell nee ...

    Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental process must be precisely regulated to satisfy cell needs at any time. We present in vivo evidence that, when growth is arrested by nutrient deprivation, cells induce rapid clearance of Pol I-Rrn3 complexes, followed by the assembly of inactive Pol I homodimers. This dual repressive mechanism reverts upon nutrient addition, thus restoring cell growth. Moreover, Pol I dimers also form after inhibition of either ribosome biogenesis or protein synthesis. Our mutational analysis, based on the electron cryomicroscopy structures of monomeric Pol I alone and in complex with Rrn3, underscores the central role of subunits A43 and A14 in the regulation of differential Pol I complexes assembly and subsequent promoter association.


    Organizational Affiliation

    IPSBB Unit, Centro de Investigaciones Biológicas, Madrid, Spain.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA135B1203Saccharomyces cerevisiae S288CMutation(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: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA14D137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA14YDR156WYD8358.11
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 cerevisiae S288CMutation(s): 0 
Gene Names: RPB5RPA7RPC9YBR154CYBR1204
Find proteins for P20434 (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 cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA43G326Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA43RRN12YOR340CO6271
Find proteins for P46669 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA12I125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA12RRN4YJR063WJ1747
Find proteins for P32529 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC2K142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC19YNL113WN1937
Find proteins for P28000 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA49M415Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA49RRN13YNL248CN0880
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA190A1664Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA190RPA1RRN1YOR341WO6276
EC: 2.7.7.6
Find proteins for P10964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10YOR210W
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA34N233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA34YJL148WJ0637
Find proteins for P47006 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC1,DNA-directed RNA polymerases I and III subunit RPAC1C380Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC40
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2013-48374-P
Ramon Areces FoundationSpain--

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection
  • Version 1.2: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Other