4C3I

Structure of 14-subunit RNA polymerase I at 3.0 A resolution, crystal form C2-100


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of the 14-Subunit RNA Polymerase I

Fernandez-Tornero, C.Moreno-Morcillo, M.Rashid, U.J.Taylor, N.M.I.Ruiz, F.M.Gruene, T.Legrand, P.Steuerwald, U.Muller, C.W.

(2013) Nature 502: 644

  • DOI: https://doi.org/10.1038/nature12636
  • Primary Citation of Related Structures:  
    4C3H, 4C3I, 4C3J

  • PubMed Abstract: 
  • Protein biosynthesis depends on the availability of ribosomes, which in turn relies on ribosomal RNA production. In eukaryotes, this process is carried out by RNA polymerase I (Pol I), a 14-subunit enzyme, the activity of which is a major determinant of cell growth ...

    Protein biosynthesis depends on the availability of ribosomes, which in turn relies on ribosomal RNA production. In eukaryotes, this process is carried out by RNA polymerase I (Pol I), a 14-subunit enzyme, the activity of which is a major determinant of cell growth. Here we present the crystal structure of Pol I from Saccharomyces cerevisiae at 3.0 Å resolution. The Pol I structure shows a compact core with a wide DNA-binding cleft and a tightly anchored stalk. An extended loop mimics the DNA backbone in the cleft and may be involved in regulating Pol I transcription. Subunit A12.2 extends from the A190 jaw to the active site and inserts a transcription elongation factor TFIIS-like zinc ribbon into the nucleotide triphosphate entry pore, providing insight into the role of A12.2 in RNA cleavage and Pol I insensitivity to α-amanitin. The A49-A34.5 heterodimer embraces subunit A135 through extended arms, thereby contacting and potentially regulating subunit A12.2.


    Organizational Affiliation

    1] Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain [2].



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA1901,664Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA1351,203Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1335Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14137Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1215Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43326Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 570Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
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DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 470Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
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DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49415Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34233Saccharomyces cerevisiaeMutation(s): 0 
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
U [auth G](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
O [auth A],
P [auth A],
Y [auth K]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

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Q [auth A]
R [auth A]
T [auth B]
V [auth I]
W [auth I]
Q [auth A],
R [auth A],
T [auth B],
V [auth I],
W [auth I],
X [auth J],
Z [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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S [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 400.53α = 90
b = 140.22β = 100.14
c = 122.89γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
SHARPphasing
BUSTERrefinement

Structure Validation

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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: 2015-07-01
    Changes: Data collection
  • Version 1.3: 2018-03-07
    Changes: Data collection