5O7X

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1016/j.cell.2017.03.003
  • Primary Citation of Related Structures:  
    5N5Y, 5N5Z, 5N60, 5N61, 5O7X

  • 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 basal Pol I initiation ...

    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. Electronic address: patrick.cramer@mpibpc.mpg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN6
A, D, G, J, M
A, D, G, J, M, P
894Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN6, YBL014C, YBL0311, YBL0312
UniProt
Find proteins for P32786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32786 
Go to UniProtKB:  P32786
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UniProt GroupP32786
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN7
B, E, H, K, N
B, E, H, K, N, Q
514Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN7, YJL025W, J1273
UniProt
Find proteins for P40992 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40992 
Go to UniProtKB:  P40992
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UniProt GroupP40992
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN11
C, F, I, L, O
C, F, I, L, O, R
507Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN11, YML043C, YM9827.09C
UniProt
Find proteins for Q04712 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04712 
Go to UniProtKB:  Q04712
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UniProt GroupQ04712
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth D]
AB [auth P]
BA [auth D]
DA [auth F]
EA [auth G]
AA [auth D],
AB [auth P],
BA [auth D],
DA [auth F],
EA [auth G],
FA [auth G],
GA [auth G],
IA [auth H],
JA [auth I],
KA [auth J],
LA [auth J],
MA [auth J],
OA [auth K],
PA [auth L],
QA [auth M],
RA [auth M],
S [auth A],
SA [auth M],
T [auth A],
TA [auth M],
U [auth A],
V [auth A],
VA [auth O],
W [auth A],
WA [auth P],
XA [auth P],
Y [auth D],
YA [auth P],
Z [auth D],
ZA [auth P]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
BB [auth P]
CA [auth D]
HA [auth G]
NA [auth J]
UA [auth M]
BB [auth P],
CA [auth D],
HA [auth G],
NA [auth J],
UA [auth M],
X [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.07α = 90.02
b = 109.14β = 90.01
c = 385.64γ = 59.98
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-08-09
    Changes: Structure summary
  • Version 1.2: 2019-10-16
    Changes: Data collection