4Y7N

The Structure Insight into 5-Carboxycytosine Recognition by RNA Polymerase II during Transcription Elongation.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.

Wang, L.Zhou, Y.Xu, L.Xiao, R.Lu, X.Chen, L.Chong, J.Li, H.He, C.Fu, X.D.Wang, D.

(2015) Nature 523: 621-625

  • DOI: https://doi.org/10.1038/nature14482
  • Primary Citation of Related Structures:  
    4Y52, 4Y7N

  • PubMed Abstract: 

    DNA methylation at selective cytosine residues (5-methylcytosine (5mC)) and their removal by TET-mediated DNA demethylation are critical for setting up pluripotent states in early embryonic development. TET enzymes successively convert 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), with 5fC and 5caC subject to removal by thymine DNA glycosylase (TDG) in conjunction with base excision repair. Early reports indicate that 5fC and 5caC could be stably detected on enhancers, promoters and gene bodies, with distinct effects on gene expression, but the mechanisms have remained elusive. Here we determined the X-ray crystal structure of yeast elongating RNA polymerase II (Pol II) in complex with a DNA template containing oxidized 5mCs, revealing specific hydrogen bonds between the 5-carboxyl group of 5caC and the conserved epi-DNA recognition loop in the polymerase. This causes a positional shift for incoming nucleoside 5'-triphosphate (NTP), thus compromising nucleotide addition. To test the implication of this structural insight in vivo, we determined the global effect of increased 5fC/5caC levels on transcription, finding that such DNA modifications indeed retarded Pol II elongation on gene bodies. These results demonstrate the functional impact of oxidized 5mCs on gene expression and suggest a novel role for Pol II as a specific and direct epigenetic sensor during transcription elongation.


  • Organizational Affiliation

    Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,733Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
UniProt
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UniProt GroupP04050
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2,DNA-directed RNA polymerase II subunit RPB21,224Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3318Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1D [auth E]215Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2E [auth F]155Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3F [auth H]146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9G [auth I]122Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5H [auth J]70Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11I [auth K]120Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4J [auth L]70Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains LengthOrganismImage
DNA (29-MER)K [auth T]29synthetic construct
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Entity ID: 12
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3')L [auth N]14synthetic construct
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Entity ID: 13
MoleculeChains LengthOrganismImage
RNA (5'-D(*AP*UP*GP*GP*AP*GP*AP*GP*G)-3')M [auth R]9synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G2P
Query on G2P

Download Ideal Coordinates CCD File 
X [auth T]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
GXTIEXDFEKYVGY-KQYNXXCUSA-N
ZN
Query on ZN

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N [auth A]
O [auth A]
R [auth B]
S [auth C]
T [auth I]
N [auth A],
O [auth A],
R [auth B],
S [auth C],
T [auth I],
U [auth I],
V [auth J],
W [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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P [auth A],
Q [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.181α = 90
b = 222.614β = 101.59
c = 192.829γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102362
Sidney Kimmel Foundation for Cancer ResearchUnited StatesKimmel Scholars award
Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSDUnited Statesstart-up funds

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
  • Version 1.3: 2017-10-04
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description