5W51

Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

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This is version 1.2 of the entry. See complete history


Literature

Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.

Wang, W.Xu, L.Hu, L.Chong, J.He, C.Wang, D.

(2017) J Am Chem Soc 139: 14436-14442

  • DOI: https://doi.org/10.1021/jacs.7b06381
  • Primary Citation of Related Structures:  
    5W4U, 5W51

  • PubMed Abstract: 

    N 6 -Methyladenine (N 6 -mA or 6 mA) is an epigenetic DNA modification in eukaryotic genomes. In contrast to the well-established roles of 5-methylcytosine for epigenetic regulation of gene expression, the functional roles of N 6 -mA remain elusive. In particular, the impact of N 6 -mA modification of the DNA template on RNA polymerase II (pol II) transcription elongation is not known. In this work, using the Saccharomyces cerevisiae pol II transcriptional elongation system as a model, we investigated the molecular mechanism of pol II recognition and processing of N 6 -mA sites via both biochemical and structural approaches. We found that N 6 -mA causes site-specific pol II pausing/stalling. Structural analysis revealed that while N 6 -mA can reach the +1 template position, the stability of the N 6 -mA and UTP base pairing is compromised. Taken together, we reveal that the presence of the 6-methyl group on adenine reduces incorporation efficiency and promotes backtracking translocation. Our studies with yeast pol II provide molecular insights into understanding the impacts of N 6 -mA on pol II transcription dynamics in different organisms.


  • Organizational Affiliation

    Department of Chemistry, Sun Yat-Sen University , Guangzhou 510275, China.


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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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
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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UniProt GroupP20434
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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
29mer template DNAK [auth T]29Saccharomyces cerevisiae
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Entity ID: 12
MoleculeChains LengthOrganismImage
14mer non-template DNAL [auth N]14Saccharomyces cerevisiae
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Entity ID: 13
MoleculeChains LengthOrganismImage
9mer RNAM [auth R]9Saccharomyces cerevisiae
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2KH
Query on 2KH

Download Ideal Coordinates CCD File 
R [auth A]5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
C9 H16 N3 O14 P3
OZIBFYOFLVBDIY-XVFCMESISA-N
ZN
Query on ZN

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N [auth A]
O [auth A]
S [auth B]
T [auth C]
U [auth I]
N [auth A],
O [auth A],
S [auth B],
T [auth C],
U [auth I],
V [auth I],
W [auth J],
X [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: 3.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.7α = 90
b = 224β = 101.04
c = 193.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description