Brand  (β version)

PDB ID: 2JA6

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Ligands
Code Name Style Show Link
MG Magnesium ion PoSSuM
ZN Zinc ion PoSSuM
Non-standard Residues
Code Name Show
BRU 5-bromo-2'-deoxyuridine-5'-monophosphate
TT [(1r,3r,4s,9r,10s,12r,15as,15br,18br,18cs)-10-hydroxy-15a,15b-dimethyl-13,15,16,18-tetraoxohexadecahydro-8h-9,12-epoxy-1,4-methano-2,5,7-trioxa-12a,14,17,18a-tetraazacyclohexadeca[1,2,3,4-def]biphenylen-3-yl]methyl dihydrogen phosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 2JA6   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE
Title : CPD lesion containing RNA Polymerase II elongation complex B
Release Data : 2007-02-20
Compound :
mol_id molecule chains synonym
1 DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT A RNA POLYMERASE II SUBUNIT 1, B220
ec: 2.7.7.6
mol_id molecule chains synonym
2 DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE B B150, RNA POLYMERASE II SUBUNIT 2
ec: 2.7.7.6
mol_id molecule chains synonym
3 DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE C B44.5
ec: 2.7.7.6
mol_id molecule chains synonym
4 DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE D B32
ec: 2.7.7.6
mol_id molecule chains synonym
5 DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE E ABC27
ec: 2.7.7.6
mol_id molecule chains synonym
6 DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE F ABC23
ec: 2.7.7.6
mol_id molecule chains synonym
7 DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE G B16
ec: 2.7.7.6
mol_id molecule chains synonym
8 DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE H ABC14.4
ec: 2.7.7.6
mol_id molecule chains synonym
9 DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 I DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE, B12.6
ec: 2.7.7.6
mol_id molecule chains synonym
10 DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 J DNA-DIRECTED RNA POLYMERASES I, II, AND III 8.3 KDA POLYPEPTIDE, ABC10-BETA, ABC8
ec: 2.7.7.6
mol_id molecule chains synonym
11 DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE K B13.6
ec: 2.7.7.6
mol_id molecule chains synonym
12 DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE L ABC10-ALPHA
ec: 2.7.7.6
mol_id molecule chains synonym
13 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3' N NONTEMPLATE DNA OF COMPLEX B
mol_id molecule chains synonym
14 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' P PRODUCT RNA OF COMPLEX B
mol_id molecule chains synonym
15 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TTP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3' T THYMINE-THYMINE CPD CONTAINING TEMPLATE DNA OF COMPLEX B
Source :
mol_id organism_scientific organism_common
1 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific organism_common
2 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific organism_common
3 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific organism_common
4 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific organism_common
5 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific organism_common
6 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific organism_common
7 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific organism_common
8 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific organism_common
9 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific organism_common
10 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific organism_common
11 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific organism_common
12 Saccharomyces cerevisiae  (taxid:4932) BAKERS' YEAST
mol_id organism_scientific
13 Synthetic construct  (taxid:32630)
synthetic: yes
other_details: SYNTHETIC OLIGONUCLEOTIDE
mol_id organism_scientific
14 Synthetic construct  (taxid:32630)
synthetic: yes
other_details: SYNTHETIC OLIGONUCLEOTIDE
mol_id organism_scientific
15 Synthetic construct  (taxid:32630)
synthetic: yes
other_details: SYNTHETIC OLIGONUCLEOTIDE
Authors : Brueckner, F., Hennecke, U., Carell, T., Cramer, P.
Keywords : DNA-DIRECTED RNA POLYMERASE, LESION RECOGNITION, TRANSFERASE/DNA/RNA, DNA DAMAGE, ZINC-FINGER, DNA-BINDING, PHOTOLESION, PHOSPHORYLATION, MISINCORPORATION, RNA POLYMERASE II, TRANSCRIPTION- COUPLED REPAIR, TCR, CPD, ZINC, ARREST, STALLING, DNA LESION, METAL-BINDING, NUCLEAR PROTEIN, TRANSCRIPTION BUBBLE, NUCLEOTIDYLTRANSFERASE, DAMAGE RECOGNITION, ELONGATION COMPLEX, TRANSFERASE, THYMINE DIMER, TRANSCRIPTION, CYCLOBUTANE PYRIMIDINE DIMER
Exp. method : X-RAY DIFFRACTION ( 4.0 Å )
Citation :

CPD damage recognition by transcribing RNA polymerase II.

Brueckner, F.,Hennecke, U.,Carell, T.  et al.
(2007)  Science  315 : 859 - 862

PubMed: 17290000
DOI: 10.1126/science.1135400

Reaction

Chain : A
UniProt : P04050 (RPB1_YEAST)
Reaction: EC: Evidence:
Physiological Direction:
a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) 2.7.7.6 -
-
Chain : B
UniProt : P08518 (RPB2_YEAST)
Reaction: EC: Evidence:
Physiological Direction:
a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) 2.7.7.6 -
-
Chain : C
UniProt : P16370 (RPB3_YEAST)
Reaction : -
Chain : D
UniProt : P20433 (RPB4_YEAST)
Reaction : -
Chain : E
UniProt : P20434 (RPAB1_YEAST)
Reaction : -
Chain : F
UniProt : P20435 (RPAB2_YEAST)
Reaction : -
Chain : G
UniProt : P34087 (RPB7_YEAST)
Reaction : -
Chain : H
UniProt : P20436 (RPAB3_YEAST)
Reaction : -
Chain : I
UniProt : P27999 (RPB9_YEAST)
Reaction : -
Chain : J
UniProt : P22139 (RPAB5_YEAST)
Reaction : -
Chain : K
UniProt : P38902 (RPB11_YEAST)
Reaction : -
Chain : L
UniProt : P40422 (RPAB4_YEAST)
Reaction : -