2JA7

CPD lesion containing RNA Polymerase II elongation complex C

Structural Biology Knowledgebase: 2JA7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.257

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2JA7

Classification: TRANSFERASE

Total Structure Weight: 1060887.50


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT A, M 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, N 1224 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB2 RPB150 RPO22 YOR151C
DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE C, O 318 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB3 YIL021W
DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE D, P 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, Q 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, R 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, S 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, T 146 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB8 YOR224C YOR50-14
DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 I, U 122 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB9 YGL070C
DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 J, V 70 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB10 YOR210W
DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE K, W 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, X 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' 1, 4 14 Synthetic construct
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TP*TTP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3' 2, 5 25 Synthetic construct
5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' 3, 6 11 Synthetic construct

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, M, N, O, U, V, X ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, M 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
2, 5 DNA LINKING C21 H29 N4 O13 P --
BRU
Query on BRU
2, 5 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: 0.275
  • R-Value Work: 0.257
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 394.36 α = 90.00
b = 221.86 β = 90.56
c = 283.11 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

  • 2015-11-04
    Type: Citation | Details: JRNL
  • 2015-11-04
    Type: Atom nomenclature | Details: HETATM
  • 2015-11-04
    Type: Function and keywords | Details: KEYWDS
  • 2015-11-04
    Type: Linkage | Details: CONECT, LINK
  • 2015-11-04
    Type: Geometry validation | Details: REMARK 500
  • 2015-11-04
    Type: Other | Details: REMARK 470, MASTER
  • 2015-11-04
    Type: Binding sites and description | Details: REMARK 800
  • 2015-11-04
    Type: Polymer description | Details: COMPND
  • 2015-11-04
    Type: Non-polymer description | Details: HET, REMARK 620
  • 2015-10-21
    Type: Biological assembly | Details: REMARK 300, REMARK 350
  • 2015-10-21
    Type: Refinement description | Details: REMARK 3
  • 2015-10-21
    Type: Other | Details: REMARK 465
  • 2015-10-21
    Type: Entry title | Details: TITLE
  • 2015-10-21
    Type: Source and taxonomy | Details: SOURCE
  • 2012-08-22
    Type: Other | Details: SSBOND
  • 2012-08-22
    Type: Version format compliance | Details: REMARK 4