5N5Y

Cryo-EM structure of RNA polymerase I in complex with Rrn3 and Core Factor (Orientation III)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 10.1016/j.cell.2017.03.003
  • Primary Citation of Related Structures:  5N5X, 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 ...

    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
DNA-directed RNA polymerase I subunit RPA190
A
1664Saccharomyces cerevisiae (strain ATCC 204508 / S288c)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: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA135
B
1203Saccharomyces cerevisiae (strain ATCC 204508 / S288c)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: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC1
C
335Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPC40 (RPC5)
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07703
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA14
D
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPA14
Find proteins for P50106 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P50106
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1
E
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPB5 (RPA7, RPC9)
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20434
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2
F
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPO26 (RPB6)
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20435
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA43
G
326Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPA43 (RRN12)
Find proteins for P46669 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P46669
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3
H
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPB8
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20436
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA12
I
125Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPA12 (RRN4)
Find proteins for P32529 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32529
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5
J
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPB10
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22139
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC2
K
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPC19
Find proteins for P28000 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P28000
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4
L
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPC10 (RPB12)
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40422
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA49
M
415Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPA49 (RRN13)
Find proteins for Q01080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q01080
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA34
N
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPA34
Find proteins for P47006 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47006
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN3
O
627Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RRN3
Find proteins for P36070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RRN3
Go to UniProtKB:  P36070
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN6
P
894Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RRN6
Find proteins for P32786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32786
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN7
Q
514Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RRN7
Find proteins for P40992 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40992
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN11
R
507Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RRN11
Find proteins for Q04712 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04712
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, I, J, L, Q
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
P, Q, R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
German Research FoundationGermanySFB860, SPP1935
The Advanced Grant TRANSREGULON from the European Research CouncilGermany693023
Volkswagen FoundationGermany--

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Structure summary
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Data collection