3HOZ

Complete RNA polymerase II elongation complex IV with a T-U mismatch and a frayed RNA 3'-guanine

Structural Biology Knowledgebase: 3HOZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.210

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3HOZ

Classification: TRANSCRIPTION TRANSFERASE / DNA / RNA HYBRID

Total Structure Weight: 535436.51


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase II subunit RPB1 A 1733 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPO21 RPB1 RPB220 SUA8 YDL140C D2150
DNA-directed RNA polymerase II subunit RPB2 B 1224 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB2 RPB150 RPO22 YOR151C
DNA-directed RNA polymerase II subunit RPB3 C 347 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB3 YIL021W
DNA-directed RNA polymerase II subunit RPB4 D 221 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB4 YJL140W J0654
DNA-directed RNA polymerases I, II, and III subunit RPABC1 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 subunit RPABC2 F 155 Saccharomyces cerevisiae EC#: 4.2.1.99 IUBMB
Gene Name(s): RPO26 RPB6 YPR187W P9677.8
DNA-directed RNA polymerase II subunit RPB7 G 171 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB7 YDR404C D9509.22
DNA-directed RNA polymerases I, II, and III subunit RPABC3 H 146 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB8 YOR224C YOR50-14
DNA-directed RNA polymerase II subunit RPB9 I 122 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB9 YGL070C
DNA-directed RNA polymerases I, II, and III subunit RPABC5 J 70 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB10 YOR210W
DNA-directed RNA polymerase II subunit RPB11 K 120 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB11 YOL005C
DNA-directed RNA polymerases I, II, and III subunit RPABC4 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'-D(*AP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3' N 12 synthetic
5'-D(*AP*GP*CP*TP*C*AP*AP*GP*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*(BRU)P*GP*GP*TP*CP*AP*TP*T)-3' T 26 synthetic
5'-R(*UP*GP*CP*AP*UP*UP*U*CP*AP*AP*CP*CP*AP*GP*GP*CP*UP*G)-3' P 18 synthetic

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

P MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
BRU
Query on BRU
T DNA LINKING C9 H12 Br N2 O8 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.210
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 221.43 α = 90.00
b = 393.75 β = 90.00
c = 281.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-06-03
  • Released Date: 2009-07-28
  • Deposition author(s): Sydow, J.F., Brueckner, F., Cheung, A.C.M., Damsma, G.E., Dengl, S., Lehmann, E., Vassylyev, D., Cramer, P.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4