5OA1

RNA polymerase I pre-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into transcription initiation by yeast RNA polymerase I.

Sadian, Y.Tafur, L.Kosinski, J.Jakobi, A.J.Wetzel, R.Buczak, K.Hagen, W.J.Beck, M.Sachse, C.Muller, C.W.

(2017) EMBO J 36: 2698-2709

  • DOI: 10.15252/embj.201796958
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi-subunit pre-initiation complex (PIC) at th ...

    In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi-subunit pre-initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo-EM structure of the 18-subunit yeast Pol I PIC bound to a transcription scaffold. The cryo-EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream DNA is positioned differently than in any previous structures of the Pol II PIC. Furthermore, the TFIIB-related subunit Rrn7 also occupies a different location compared to the Pol II PIC although it uses similar interfaces as TFIIB to contact DNA. Our results show that although general features of eukaryotic transcription initiation are conserved, Pol I and Pol II use them differently in their respective transcription initiation complexes.


    Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany cmueller@embl.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA190A1664Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA190RPA1RRN1YOR341WO6276
EC: 2.7.7.6
Find proteins for P10964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10964 
Go to UniProtKB:  P10964
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC1C335Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC40RPC5YPR110CP8283.18
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07703 
Go to UniProtKB:  P07703
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA14D137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA14YDR156WYD8358.11
Find proteins for P50106 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50106 
Go to UniProtKB:  P50106
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5RPA7RPC9YBR154CYBR1204
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20434 
Go to UniProtKB:  P20434
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20435 
Go to UniProtKB:  P20435
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20436 
Go to UniProtKB:  P20436
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA12I125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA12RRN4YJR063WJ1747
Find proteins for P32529 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32529 
Go to UniProtKB:  P32529
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10YOR210W
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22139 
Go to UniProtKB:  P22139
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC2K142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC19YNL113WN1937
Find proteins for P28000 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28000 
Go to UniProtKB:  P28000
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40422 
Go to UniProtKB:  P40422
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA49M415Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA49RRN13YNL248CN0880
Find proteins for Q01080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01080 
Go to UniProtKB:  Q01080
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA34N233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA34YJL148WJ0637
Find proteins for P47006 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47006 
Go to UniProtKB:  P47006
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN3O627Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN3YKL125W
Find proteins for P36070 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36070 
Go to UniProtKB:  P36070
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN7U514Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN7YJL025WJ1273
Find proteins for P40992 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40992 
Go to UniProtKB:  P40992
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN11W507Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN11YML043CYM9827.09C
Find proteins for Q04712 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04712 
Go to UniProtKB:  Q04712
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA113Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA219Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA3, 99Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA424Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA5, Q16Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA6, 810Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA725Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAP22Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAY12Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAR27Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase I-specific transcription initiation factor RRN6V894Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN6YBL014CYBL0311YBL0312
Find proteins for P32786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32786 
Go to UniProtKB:  P32786
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA135B1203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA135RPA2RRN2SRP3YPR010CYP9531.03C
EC: 2.7.7.6
Find proteins for P22138 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22138 
Go to UniProtKB:  P22138
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAZ15Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA43G326Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA43RRN12YOR340CO6271
Find proteins for P46669 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46669 
Go to UniProtKB:  P46669
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 17
MoleculeChainsLengthOrganism
DNA (56-MER)T70Saccharomyces cerevisiae S288C

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 16
MoleculeChainsLengthOrganism
DNA (49-MER)S70Saccharomyces cerevisiae S288C
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2017-12-06
    Changes: Advisory, Database references
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations