5O7X

CRYSTAL STRUCTURE OF S. CEREVISIAE CORE FACTOR AT 3.2A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis of RNA Polymerase I Transcription Initiation.

Engel, C.Gubbey, T.Neyer, S.Sainsbury, S.Oberthuer, C.Baejen, C.Bernecky, C.Cramer, P.

(2017) Cell 169: 120-131.e22

  • DOI: 10.1016/j.cell.2017.03.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for ...

    Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct "bendability" and "meltability" of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase.


    Organizational Affiliation

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN6
A, D, G, J, M, P
894Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRN6
Find proteins for P32786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32786
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN7
B, E, H, K, N, Q
514Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRN7
Find proteins for P40992 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40992
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN11
C, F, I, L, O, R
507Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRN11
Find proteins for Q04712 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04712
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D, F, G, H, I, J, K, L, M, O, P
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, D, G, J, M, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.254 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 109.070α = 90.02
b = 109.140β = 90.01
c = 385.640γ = 59.98
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Structure summary