4C2M

Structure of RNA polymerase I at 2.8 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

RNA Polymerase I Structure and Transcription Regulation.

Engel, C.Sainsbury, S.Cheung, A.C.Kostrewa, D.Cramer, P.

(2013) Nature 502: 502

  • DOI: 10.1038/nature12712
  • Primary Citation of Related Structures:  
    4C2M

  • PubMed Abstract: 
  • Transcription of ribosomal RNA by RNA polymerase (Pol) I initiates ribosome biogenesis and regulates eukaryotic cell growth. The crystal structure of Pol I from the yeast Saccharomyces cerevisiae at 2.8 Å resolution reveals all 14 subunits of the 590-kilodalton enzyme, and shows differences to Pol II ...

    Transcription of ribosomal RNA by RNA polymerase (Pol) I initiates ribosome biogenesis and regulates eukaryotic cell growth. The crystal structure of Pol I from the yeast Saccharomyces cerevisiae at 2.8 Å resolution reveals all 14 subunits of the 590-kilodalton enzyme, and shows differences to Pol II. An 'expander' element occupies the DNA template site and stabilizes an expanded active centre cleft with an unwound bridge helix. A 'connector' element invades the cleft of an adjacent polymerase and stabilizes an inactive polymerase dimer. The connector and expander must detach during Pol I activation to enable transcription initiation and cleft contraction by convergent movement of the polymerase 'core' and 'shelf' modules. Conversion between an inactive expanded and an active contracted polymerase state may generally underlie transcription. Regulatory factors can modulate the core-shelf interface that includes a 'composite' active site for RNA chain initiation, elongation, proofreading and termination.


    Organizational Affiliation

    Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4A [auth 1], P [auth L]70Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40422 
Go to UniProtKB:  P40422
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49B [auth 2], Q [auth M]415Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q01080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01080 
Go to UniProtKB:  Q01080
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34C [auth 3], R [auth N]233Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P47006 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47006 
Go to UniProtKB:  P47006
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43D [auth 4], K [auth G], S [auth O], Z [auth V]326Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P46669 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46669 
Go to UniProtKB:  P46669
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190E [auth A], T [auth P]1664Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P10964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10964 
Go to UniProtKB:  P10964
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135F [auth B], U [auth Q]1203Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P22138 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22138 
Go to UniProtKB:  P22138
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1G [auth C], V [auth R]335Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07703 
Go to UniProtKB:  P07703
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14H [auth D], W [auth S]137Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P50106 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50106 
Go to UniProtKB:  P50106
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1I [auth E], X [auth T]215Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20434 
Go to UniProtKB:  P20434
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2J [auth F], Y [auth U]155Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20435 
Go to UniProtKB:  P20435
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3L [auth H], AA [auth W]146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20436 
Go to UniProtKB:  P20436
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12M [auth I], BA [auth X]125Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32529 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32529 
Go to UniProtKB:  P32529
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5N [auth J], CA [auth Y]70Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22139 
Go to UniProtKB:  P22139
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2O [auth K], DA [auth Z]142Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P28000 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28000 
Go to UniProtKB:  P28000
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
HA [auth B], PA [auth Q]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EA [auth 1] , FA [auth A] , GA [auth A] , IA [auth B] , JA [auth I] , KA [auth I] , LA [auth J] , MA [auth L] , 
EA [auth 1], FA [auth A], GA [auth A], IA [auth B], JA [auth I], KA [auth I], LA [auth J], MA [auth L], NA [auth P], OA [auth P], QA [auth Q], RA [auth X], SA [auth X], TA [auth Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.74α = 108.06
b = 139.02β = 95.4
c = 209.55γ = 93.85
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
autoSHARPphasing
PARROTphasing
PHENIXrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Database references
  • Version 1.2: 2015-08-19
    Changes: Derived calculations