4C2M

Structure of RNA polymerase I at 2.8 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 

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

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
1, L
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC10 (RPB12)
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40422
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
2, M
415Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPA49 (RRN13)
Find proteins for Q01080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q01080
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
3, N
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPA34
Find proteins for P47006 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47006
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
4, G, O, V
326Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPA43 (RRN12)
Find proteins for P46669 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P46669
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190
A, P
1664Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPA190 (RPA1, RRN1)
EC: 2.7.7.6
Find proteins for P10964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P10964
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135
B, Q
1203Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPA135 (RPA2, RRN2, SRP3)
EC: 2.7.7.6
Find proteins for P22138 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22138
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
C, R
335Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC40 (RPC5)
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07703
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14
D, S
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPA14
Find proteins for P50106 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P50106
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
E, T
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB5 (RPA7, RPC9)
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20434
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
F, U
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO26 (RPB6)
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20435
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
H, W
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB8
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20436
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
I, X
125Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPA12 (RRN4)
Find proteins for P32529 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32529
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
J, Y
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB10
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22139
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
K, Z
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC19
Find proteins for P28000 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P28000
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
1, A, B, I, J, L, P, Q, X, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
B, Q
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 122.740α = 108.06
b = 139.020β = 95.40
c = 209.550γ = 93.85
Software Package:
Software NamePurpose
PARROTphasing
XDSdata scaling
PHENIXrefinement
autoSHARPphasing
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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