2JA7

CPD lesion containing RNA Polymerase II elongation complex C

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Cpd Damage Recognition by Transcribing RNA Polymerase II.

Brueckner, F., Hennecke, U., Carell, T., Cramer, P.

(2007) Science 315: 859

  • DOI: 10.1126/science.1135400
  • Primary Citation of Related Structures:  
    2JA5, 2JA6, 2JA7, 2JA8

  • PubMed Abstract: 

    • Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light-induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II ...

    Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light-induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II. A CPD in the transcribed strand slowly passes a translocation barrier and enters the polymerase active site. The CPD 5'-thymine then directs uridine misincorporation into messenger RNA, which blocks translocation. Artificial replacement of the uridine by adenosine enables CPD bypass; thus, Pol II stalling requires CPD-directed misincorporation. In the stalled complex, the lesion is inaccessible, and the polymerase conformation is unchanged. This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II.

    Organizational Affiliation: 

    Munich Center for Integrated Protein Science CiPS, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNITG [auth A],
S [auth M]		1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDEH [auth B],
T [auth N]		1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDEI [auth C],
U [auth O]		318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDEJ [auth D],
V [auth P]		221Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDEK [auth E],
W [auth Q]		215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDEL [auth F],
X [auth R]		155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDEM [auth G],
Y [auth S]		171Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDEN [auth H],
Z [auth T]		146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9O [auth I],
AA [auth U]		122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10P [auth J],
BA [auth V]		70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDEQ [auth K],
CA [auth W]		120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDER [auth L],
DA [auth X]		70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3'A [auth 1],
D [auth 4]		14synthetic construct
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Entity ID: 2
MoleculeChainsLengthOrganismImage
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'B [auth 2],
E [auth 5]		25synthetic construct
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3'C [auth 3],
F [auth 6]		11synthetic construct
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
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FA [auth A],
GA [auth A],
HA [auth B],
IA [auth C],
JA [auth I],
FA [auth A],
GA [auth A],
HA [auth B],
IA [auth C],
JA [auth I],
KA [auth I],
LA [auth J],
MA [auth L],
NA [auth M],
OA [auth M],
QA [auth N],
RA [auth O],
SA [auth U],
TA [auth U],
UA [auth V],
VA [auth X]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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EA [auth A],
PA [auth M]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 394.358α = 90
b = 221.862β = 90.56
c = 283.105γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2012-08-22
    Changes: Other, Version format compliance
  • Version 1.2: 2015-10-21
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2015-11-04
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary