6U90

Crystal structure of DNMT3B(N779A)-DNMT3L in complex with CpGpT DNA

• PDB DOI: https://doi.org/10.2210/pdb6U90/pdb
• NAKB: 6U90

• Classification: Transferase/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-09-06 Released: 2020-06-10 
• Deposition Author(s): Gao, L., Song, J.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms

Gao, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 130.97 kDa 
• Atom Count: 8,631 
• Modelled Residue Count: 1,018 
• Deposited Residue Count: 1,050 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3B	A, D	291	Homo sapiens	Mutation(s): 1  Gene Names: DNMT3B EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBC3 (Homo sapiens) Explore Q9UBC3  Go to UniProtKB:  Q9UBC3
PHAROS:  Q9UBC3 GTEx:  ENSG00000088305

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3-like	B, C	209	Homo sapiens	Mutation(s): 0  Gene Names: DNMT3L
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJW3 (Homo sapiens) Explore Q9UJW3  Go to UniProtKB:  Q9UJW3
PHAROS:  Q9UJW3 GTEx:  ENSG00000142182

Entity ID: 3
Molecule	Chains	Length	Organism	Image
CpGpT DNA (25-MER)	E, F	25	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	H [auth A], J [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	G [auth A], I [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	BindingDB:  6U90	IC50: min: 200, max: 5.00e+4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.506	α = 90
b = 191.506	β = 90
c = 49.597	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Gao, L., Song, J.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	1R35GM119721

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-12-25
  Changes: Advisory, Data collection, Derived calculations, Structure summary