3H3V

Yeast RNAP II containing poly(A)-signal sequence in the active site

Structural Biology Knowledgebase: 3H3V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.0 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3H3V

Classification: TRANSFERASE / DNA / RNA

Total Structure Weight: 531999.18


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase II subunit RPB1 B 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 C 1224 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB2 RPB150 RPO22 YOR151C
DNA-directed RNA polymerase II subunit RPB3 D 318 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB3 YIL021W
DNA-directed RNA polymerase II subunit RPB4 E 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 F 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 G 155 Saccharomyces cerevisiae EC#: 4.2.1.99 IUBMB
Gene Name(s): RPO26 RPB6 YPR187W P9677.8
DNA-directed RNA polymerase II subunit RPB7 H 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 I 146 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB8 YOR224C YOR50-14
DNA-directed RNA polymerase II subunit RPB9 J 122 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB9 YGL070C
DNA-directed RNA polymerases I, II, and III subunit RPABC5 K 70 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB10 YOR210W
DNA-directed RNA polymerase II subunit RPB11 L 120 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB11 YOL005C
DNA-directed RNA polymerases I, II, and III subunit RPABC4 M 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*GP*CP*TP*CP*AP*AP*GP*TP*AP*GP*CP*TP*GP*CP*TP*TP*TP*AP*TP*TP*GP*CP*AP*TP*T)-3' N 14 synthetic
5'-D(*CP*AP*GP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3' P 16 synthetic
5'-R(*UP*GP*CP*AP*UP*UP*UP*CP*GP*CP*AP*AP*UP*AP*AP*A)-3' T 26 synthetic

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

B, C, D, J, K, M ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B 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: 0.241
  • R-Value Work: 0.205
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 222.47 α = 90.00
b = 391.62 β = 90.00
c = 284.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-04-17
  • Released Date: 2009-06-16
  • Deposition author(s): Dengl, S., Cramer, P.

Revision History

  • 2013-11-06
    Type: Data collection | Details: update wavelength
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4