6W8W | pdb_00006w8w

Crystal structure of mouse DNMT1 in complex with CCG DNA

• PDB DOI: https://doi.org/10.2210/pdb6W8W/pdb
• NAKB: 6W8W

• Classification: TRANSFERASE/DNA
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-21 Released: 2020-07-08 
• Deposition Author(s): Anteneh, H., Song, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.280 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

DNMT1 activity, base flipping mechanism and genome-wide DNA methylation are regulated by the DNA sequence context

Adam, S., Anteneh, H., Hornisch, M., Wagner, V., Lu, J., Radde, N.E., Bashtrykov, P., Song, J., Jeltsch, A.

(2020) Nat Commun 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 213.8 kDa 
• Atom Count: 13,939 
• Modeled Residue Count: 1,702 
• Deposited Residue Count: 1,794 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 1	A, B	873	Mus musculus	Mutation(s): 0  Gene Names: Dnmt1, Dnmt, Met1, Uim EC: 2.1.1.37
UniProt
Find proteins for P13864 (Mus musculus) Explore P13864  Go to UniProtKB:  P13864

Entity ID: 2
Molecule	Chains	Length	Organism	Image
CCG DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')	C, D [auth E]	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
CCG DNA (5'-D(*CP*CP*TP*TP*CP*(C49)P*GP*TP*AP*AP*GP*T)-3')	E [auth D], F	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	G [auth A], J [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN (Subject of Investigation/LOI)	H [auth A], I [auth A], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.280 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.794	α = 90
b = 152.593	β = 94.74
c = 95.631	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Anteneh, H., Song, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM119721

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Data collection, Structure summary