3GTO

Backtracked RNA polymerase II complex with 15mer RNA

Structural Biology Knowledgebase: 3GTO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.0 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.269

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3GTO

Classification: TRANSCRIPTION TRANSFERASE / DNA-RNA HYBRID

Total Structure Weight: 487852.47


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase II subunit RPB1 A 1733 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Fragment: DNA-directed RNA polymerase II largest subunit
Gene Name(s): RPO21 RPB1 RPB220 SUA8 YDL140C D2150
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase II subunit RPB2 B 1224 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Fragment: DNA-directed RNA polymerase II 140 kDa polypeptide
Gene Name(s): RPB2 RPB150 RPO22 YOR151C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase II subunit RPB3 C 318 Saccharomyces cerevisiae Fragment: DNA-directed RNA polymerase II 45 kDa polypeptide
Gene Name(s): RPB3 YIL021W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC1 E 215 Saccharomyces cerevisiae Fragment: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
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
Fragment: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
Gene Name(s): RPO26 RPB6 YPR187W P9677.8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC3 H 146 Saccharomyces cerevisiae Fragment: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
Gene Name(s): RPB8 YOR224C YOR50-14
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase II subunit RPB9 I 122 Saccharomyces cerevisiae Fragment: DNA-directed RNA polymerase II subunit 9
Gene Name(s): RPB9 YGL070C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC5 J 70 Saccharomyces cerevisiae Fragment: DNA-directed RNA polymerases I/II/III subunit 10
Gene Name(s): RPB10 YOR210W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase II subunit RPB11 K 120 Saccharomyces cerevisiae Fragment: DNA-directed RNA polymerase II 13.6 kDa polypeptide
Gene Name(s): RPB11 YOL005C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerases I, II, and III subunit RPABC4 L 70 Saccharomyces cerevisiae Fragment: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
Gene Name(s): RPC10 RPB12 YHR143W-A YHR143BW
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*AP*UP*GP*CP*AP*C)-3') R 15 synthetic RNA strand
DNA (28-MER) T 28 synthetic DNA template strand
DNA (5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3') N 14 synthetic DNA non-template strand

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

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.0 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.269
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 170.85 α = 90.00
b = 222.80 β = 101.98
c = 194.98 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-03-27
  • Released Date: 2009-06-09
  • Deposition author(s): Wang, D., Bushnell, D.A., Huang, X., Westover, K.D., Levitt, M., Kornberg, R.D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor