5OT2

RNA polymerase II elongation complex in the presence of 3d-Napht-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanism of RNA polymerase II stalling by DNA alkylation.

Malvezzi, S.Farnung, L.Aloisi, C.M.N.Angelov, T.Cramer, P.Sturla, S.J.

(2017) Proc Natl Acad Sci U S A 114: 12172-12177

  • DOI: 10.1073/pnas.1706592114
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Several anticancer agents that form DNA adducts in the minor groove interfere with DNA replication and transcription to induce apoptosis. Therapeutic resistance can occur, however, when cells are proficient in the removal of drug-induced damage. Acyl ...

    Several anticancer agents that form DNA adducts in the minor groove interfere with DNA replication and transcription to induce apoptosis. Therapeutic resistance can occur, however, when cells are proficient in the removal of drug-induced damage. Acylfulvenes are a class of experimental anticancer agents with a unique repair profile suggesting their capacity to stall RNA polymerase (Pol) II and trigger transcription-coupled nucleotide excision repair. Here we show how different forms of DNA alkylation impair transcription by RNA Pol II in cells and with the isolated enzyme and unravel a mode of RNA Pol II stalling that is due to alkylation of DNA in the minor groove. We incorporated a model for acylfulvene adducts, the stable 3-deaza-3-methoxynaphtylethyl-adenosine analog (3d-Napht-A), and smaller 3-deaza-adenosine analogs, into DNA oligonucleotides to assess RNA Pol II transcription elongation in vitro. RNA Pol II was strongly blocked by a 3d-Napht-A analog but bypassed smaller analogs. Crystal structure analysis revealed that a DNA base containing 3d-Napht-A can occupy the +1 templating position and impair closing of the trigger loop in the Pol II active center and polymerase translocation into the next template position. These results show how RNA Pol II copes with minor-groove DNA alkylation and establishes a mechanism for drug resistance.


    Organizational Affiliation

    Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland; patrick.cramer@mpibpc.mpg.de sturlas@ethz.ch.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB4D221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB4YJL140WJ0654
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB7G171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB7YDR404CD9509.22
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9I122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB9YGL070C
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB11K120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB11YOL005C
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB1A1733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO21RPB1RPB220SUA8YDL140CD2150
EC: 2.7.7.6
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10YOR210W
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB2B1224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB2RPB150RPO22YOR151C
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB3C318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB3YIL021W
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5RPA7RPC9YBR154CYBR1204
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  • Reference Sequence
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Entity ID: 14
MoleculeChainsLengthOrganism
DNA non-template strandN14synthetic construct
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Entity ID: 15
MoleculeChainsLengthOrganism
RNA product strandP11synthetic construct

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Entity ID: 13
MoleculeChainsLengthOrganism
DNA template strandT26synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AHW
Query on AHW

Download CCD File 
T
2-ethyl-7-methoxy-naphthalene
C13 H14 O
IZQPFGFFOUIMRX-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 221.35α = 90
b = 394.93β = 90
c = 283.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-07-10
    Changes: Data collection