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

Literature

Macromolecules
Sequence Display for 5N5Y

Classification: TRANSCRIPTION

Total Structure Weight: 885697.38

Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase I subunit RPA190 A 1664 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPA190 RPA1 Gene View RRN1 YOR341W O6276
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase I subunit RPA135 B 1203 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPA135 RPA2 Gene View RRN2 SRP3 YPR010C YP9531.03C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I and III subunit RPAC1 C 335 Saccharomyces cerevisiae Gene Name(s): RPC40 RPC5 YPR110C P8283.18
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase I subunit RPA14 D 137 Saccharomyces cerevisiae Gene Name(s): RPA14 YDR156W YD8358.11
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC1 E 215 Saccharomyces cerevisiae Gene Name(s): RPB5 RPA7 RPC9 YBR154C YBR1204
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC2 F 155 Saccharomyces cerevisiae EC#: 4.2.1.99 IUBMB
Gene Name(s): RPO26 RPB6 YPR187W P9677.8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase I subunit RPA43 G 326 Saccharomyces cerevisiae Gene Name(s): RPA43 RRN12 YOR340C O6271
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC3 H 146 Saccharomyces cerevisiae Gene Name(s): RPB8 YOR224C YOR50-14
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase I subunit RPA12 I 125 Saccharomyces cerevisiae Gene Name(s): RPA12 RRN4 YJR063W J1747
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC5 J 70 Saccharomyces cerevisiae Gene Name(s): RPB10 YOR210W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I and III subunit RPAC2 K 142 Saccharomyces cerevisiae Gene Name(s): RPC19 YNL113W N1937
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC4 L 70 Saccharomyces cerevisiae Gene Name(s): RPC10 RPB12 YHR143W-A YHR143BW
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase I subunit RPA49 M 415 Saccharomyces cerevisiae Gene Name(s): RPA49 RRN13 YNL248C N0880
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase I subunit RPA34 N 233 Saccharomyces cerevisiae Gene Name(s): RPA34 YJL148W J0637
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase I-specific transcription initiation factor RRN3 O 627 Saccharomyces cerevisiae Gene Name(s): RRN3 Gene View YKL125W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase I-specific transcription initiation factor RRN6 P 894 Saccharomyces cerevisiae Gene Name(s): RRN6 YBL014C YBL0311 YBL0312
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase I-specific transcription initiation factor RRN7 Q 514 Saccharomyces cerevisiae Gene Name(s): RRN7 YJL025W J1273
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase I-specific transcription initiation factor RRN11 R 507 Saccharomyces cerevisiae Gene Name(s): RRN11 YML043C YM9827.09C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

P, Q, R SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, I, J, L, Q ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

R MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.7 Å
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-02-14
  • Released Date: 2017-04-05
  • Deposition author(s): Engel, C., Gubbey, T., Neyer, S., Sainsbury, S., Oberthuer, C., Baejen, C., Bernecky, C., Cramer, P.

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