2JA8

CPD lesion containing RNA Polymerase II elongation complex D

Structural Biology Knowledgebase: 2JA8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.269

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2JA8

Classification: TRANSFERASE

Total Structure Weight: 530419.75


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 45KDA POLYPEPTIDE C 318 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB3 YIL021W
DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE D 221 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB4 YJL140W J0654
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 POLYMERASE II 19KDA POLYPEPTIDE 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 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'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3' N 14 Synthetic construct
5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*AP*UP)-3' P 11 Synthetic construct
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TP*TP*TTP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3' T 25 Synthetic construct

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

A 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)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
TT
Query on TT
T DNA LINKING C21 H29 N4 O13 P --
BRU
Query on BRU
T DNA LINKING C9 H12 Br N2 O8 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.269
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 222.64 α = 90.00
b = 392.85 β = 90.00
c = 282.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-11-23
  • Released Date: 2007-02-20
  • Deposition author(s): Brueckner, F., Hennecke, U., Carell, T., Cramer, P.

Revision History

  • 2015-05-20
    Type: Polymer description | Details: COMPND
  • 2015-05-20
    Type: Refinement description | Details: REMARK 3
  • 2015-05-20
    Type: Citation | Details: JRNL
  • 2015-05-20
    Type: Entry title | Details: TITLE
  • 2015-05-20
    Type: Version format compliance | Details: REMARK 4
  • 2015-05-20
    Type: Function and keywords | Details: KEYWDS
  • 2015-05-20
    Type: Source and taxonomy | Details: SOURCE
  • 2015-05-20
    Type: Other | Details: REMARK 465,REMARK 470,MASTER,MODRES
  • 2015-05-20
    Type: Biological assembly | Details: REMARK 350