4A93

RNA Polymerase II elongation complex containing a CPD Lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of Translesion Transcription by RNA Polymerase II and its Role in Cellular Resistance to DNA Damage.

Walmacq, C.Cheung, A.C.Kireeva, M.L.Lubkowska, L.Ye, C.Gotte, D.Strathern, J.N.Carell, T.Cramer, P.Kashlev, M.

(2012) Mol.Cell 46: 18

  • DOI: 10.1016/j.molcel.2012.02.006

  • PubMed Abstract: 
  • UV-induced cyclobutane pyrimidine dimers (CPDs) in the template DNA strand stall transcription elongation by RNA polymerase II (Pol II). If the nucleotide excision repair machinery does not promptly remove the CPDs, stalled Pol II creates a roadblock ...

    UV-induced cyclobutane pyrimidine dimers (CPDs) in the template DNA strand stall transcription elongation by RNA polymerase II (Pol II). If the nucleotide excision repair machinery does not promptly remove the CPDs, stalled Pol II creates a roadblock for DNA replication and subsequent rounds of transcription. Here we present evidence that Pol II has an intrinsic capacity for translesion synthesis (TLS) that enables bypass of the CPD with or without repair. Translesion synthesis depends on the trigger loop and bridge helix, the two flexible regions of the Pol II subunit Rpb1 that participate in substrate binding, catalysis, and translocation. Substitutions in Rpb1 that promote lesion bypass in vitro increase UV resistance in vivo, and substitutions that inhibit lesion bypass decrease cell survival after UV irradiation. Thus, translesion transcription becomes essential for cell survival upon accumulation of the unrepaired CPD lesions in genomic DNA.


    Organizational Affiliation

    NCI Center for Cancer Research, Frederick, MD 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
A
1732Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO21 (RPB1, RPB220, SUA8)
EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04050
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
B
1224Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB2 (RPB150, RPO22)
EC: 2.7.7.6
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08518
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
C
318Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB3
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16370
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
D
221Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB4
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20433
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
E
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB5 (RPA7, RPC9)
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20434
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
F
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO26 (RPB6)
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20435
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
G
171Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB7
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P34087
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
H
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB8
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20436
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
I
122Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB9
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P27999
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
J
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB10
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22139
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
K
120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB11
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38902
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
L
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC10 (RPB12)
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40422
Entity ID: 13
MoleculeChainsLengthOrganism
5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*TP)-3'N14Saccharomyces cerevisiae
Entity ID: 14
MoleculeChainsLengthOrganism
5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP*AP)-3'P12Saccharomyces cerevisiae
Entity ID: 15
MoleculeChainsLengthOrganism
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*T*TTP*TP*TP*CP*C BRUP*GP*GP*TP*CP*AP*TP*T)-3'T25Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
T
DNA LINKINGC9 H12 Br N2 O8 PDU
TT
Query on TT
T
DNA LINKINGC21 H29 N4 O13 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 221.637α = 90.00
b = 391.519β = 90.00
c = 281.774γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-25
    Type: Other
  • Version 1.2: 2012-11-21
    Type: Other