7R77 | pdb_00007r77

Cryo-EM structure of DNMT5 binary complex with hemimethylated DNA

• PDB DOI: https://doi.org/10.2210/pdb7R77/pdb
• EM Map EMD-24294: EMDB EMDataResource
• NAKB: 7R77

• Classification: TRANSFERASE/DNA
• Organism(s): Cryptococcus neoformans H99, Cryptococcus neoformans
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2021-06-24 Released: 2022-02-23 
• Deposition Author(s): Wang, J., Patel, D.J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

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

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

• PubMed: 35202575 
• DOI: https://doi.org/10.1016/j.molcel.2022.01.028
• Primary Citation 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.

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Organizational Affiliation: 
• Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: [e-mail].
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address: [e-mail].
Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 286.31 kDa 
• Atom Count: 14,980 
• Modeled Residue Count: 1,855 
• Deposited Residue Count: 2,420 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein Rad8	A	2,348	Cryptococcus neoformans H99	Mutation(s): 0  Gene Names: CNAG_07552 EC: 3.6.4
UniProt
Find proteins for J9VI03 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VI03  Go to UniProtKB:  J9VI03

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*G)-3')	B	36	Cryptococcus neoformans

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*G)-3')	C [auth D]	36	Cryptococcus neoformans

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-23 
Deposition Author(s): Wang, J., Patel, D.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30CA008748

Revision History  

• 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