2NVQ

RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP

Structural Biology Knowledgebase: 2NVQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.283
  • R-Value Work: 0.229

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2NVQ

Classification: TRANSCRIPTION TRANSFERASE / DNA-RNA HYBRID

Total Structure Weight: 486753.38


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase II largest subunit A 1733 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPO21 RPB1 RPB220 SUA8 YDL140C D2150
DNA-directed RNA polymerase II 140 kDa polypeptide B 1224 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB2 RPB150 RPO22 YOR151C
DNA-directed RNA polymerase II 45 kDa polypeptide C 318 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB3 YIL021W
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide E 215 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB5 RPA7 RPC9 YBR154C YBR1204
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide F 155 Saccharomyces cerevisiae EC#: 4.2.1.99 IUBMB
Gene Name(s): RPO26 RPB6 YPR187W P9677.8
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide H 146 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB8 YOR224C YOR50-14
DNA-directed RNA polymerase II subunit 9 I 122 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB9 YGL070C
DNA-directed RNA polymerases I/II/III subunit 10 J 70 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB10 YOR210W
DNA-directed RNA polymerase II 13.6 kDa polypeptide K 120 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB11 YOL005C
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide L 70 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPC10 RPB12 YHR143W-A YHR143BW
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3' R 10 Synthetic construct
28-MER DNA template strand T 28 Synthetic construct
5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3' N 14 Synthetic construct

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

T DEOXYURIDINE-5'-TRIPHOSPHATE
C9 H15 N2 O14 P3
AHCYMLUZIRLXAA-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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: 2.9 Å
  • R-Value Free: 0.283
  • R-Value Work: 0.229
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 170.65 α = 90.00
b = 222.76 β = 101.31
c = 195.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-11-13
  • Released Date: 2006-12-12
  • Deposition author(s): Wang, D., Bushnell, D.A., Westover, K.D., Kaplan, C.D., Kornberg, R.D.

Revision History

  • 2015-05-27
    Type: Linkage | Details: remove SSBOND
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4