3S1R

RNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soaked with GTP

Structural Biology Knowledgebase: 3S1R SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3S1R

Classification: TRANSCRIPTION / RNA / DNA

Total Structure Weight: 481212.09


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 318 Saccharomyces cerevisiae Gene Name(s): RPB3 YIL021W
DNA-directed RNA polymerases I, II, and III subunit RPABC1 E 215 Saccharomyces cerevisiae 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 polymerases I, II, and III subunit RPABC3 H 146 Saccharomyces cerevisiae Gene Name(s): RPB8 YOR224C YOR50-14
DNA-directed RNA polymerase II subunit RPB9 I 122 Saccharomyces cerevisiae Gene Name(s): RPB9 YGL070C
DNA-directed RNA polymerases I, II, and III subunit RPABC5 J 70 Saccharomyces cerevisiae Gene Name(s): RPB10 YOR210W
DNA-directed RNA polymerase II subunit RPB11 K 120 Saccharomyces cerevisiae Gene Name(s): RPB11 YOL005C
DNA-directed RNA polymerases I, II, and III subunit RPABC4 L 70 Saccharomyces cerevisiae Gene Name(s): RPC10 RPB12 YHR143W-A YHR143BW
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*AP*GP*AP*GP*G*)-3') R 5 synthetic 3'-deoxy RNA (5-nt)
DNA (5'-D(*CP*TP*AP*CP*CP*GP*AP*TP*AP*AP*GP*CP*AP*GP*AP*CP*GP*AP*TP*CP*CP*TP*CP*TP*CP*GP*AP*TP*G)-3') T 29 synthetic Template DNA

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

R GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-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: 3.2 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.177
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 160.67 α = 90.00
b = 221.32 β = 98.31
c = 193.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-16
  • Released Date: 2011-08-10
  • Deposition author(s): Liu, X., Bushnell, D.A., Silva, D.A., Huang, X., Kornberg, R.D.

Revision History

No revisions since initial release