7R77

Cryo-EM structure of DNMT5 binary complex with hemimethylated DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance.

Wang, J.Catania, S.Wang, C.de la Cruz, M.J.Rao, B.Madhani, H.D.Patel, D.J.

(2022) Mol Cell 82: 1186-1198.e6

  • DOI: https://doi.org/10.1016/j.molcel.2022.01.028
  • Primary Citation of Related Structures:  
    7R76, 7R77, 7R78, 7T02

  • PubMed Abstract: 

    Epigenetic evolution occurs over million-year timescales in Cryptococcus neoformans and is mediated by DNMT5, the first maintenance type cytosine methyltransferase identified in the fungal or protist kingdoms, the first dependent on adenosine triphosphate (ATP), and the most hemimethyl-DNA-specific enzyme known. To understand these novel properties, we solved cryo-EM structures of CnDNMT5 in three states. These studies reveal an elaborate allosteric cascade in which hemimethylated DNA binding first activates the SNF2 ATPase domain by a large rigid body rotation while the target cytosine partially flips out of the DNA duplex. ATP binding then triggers striking structural reconfigurations of the methyltransferase catalytic pocket to enable cofactor binding, completion of base flipping, and catalysis. Bound unmethylated DNA does not open the catalytic pocket and is instead ejected upon ATP binding, driving high fidelity. This unprecedented chaperone-like, enzyme-remodeling role of the SNF2 ATPase domain illuminates how energy is used to enable faithful epigenetic memory.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: wangj1@mskcc.org.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein Rad82,348Cryptococcus neoformans var. grubii H99Mutation(s): 0 
Gene Names: CNAG_07552
EC: 3.6.4
UniProt
Find proteins for J9VI03 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VI03 
Go to UniProtKB:  J9VI03
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9VI03
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*G)-3')36Cryptococcus neoformans
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*G)-3')C [auth D]36Cryptococcus neoformans
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA008748

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references
  • Version 1.2: 2022-03-30
    Changes: Database references
  • Version 1.3: 2024-06-05
    Changes: Data collection