6U8X

Crystal structure of DNMT3B-DNMT3L in complex with CpApG DNA

  • Classification: Transferase/DNA
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • 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: 2.95 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation 3D Report Full Report



Literature

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

Gao, L.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA (cytosine-5)-methyltransferase 3B
A, D
291Homo sapiensMutation(s): 0 
Gene Names: DNMT3B
EC: 2.1.1.37
Find proteins for Q9UBC3 (Homo sapiens)
Go to UniProtKB:  Q9UBC3
NIH Common Fund Data Resources
PHAROS  Q9UBC3
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA (cytosine-5)-methyltransferase 3-like
B, C
209Homo sapiensMutation(s): 0 
Gene Names: DNMT3L
Find proteins for Q9UJW3 (Homo sapiens)
Go to UniProtKB:  Q9UJW3
NIH Common Fund Data Resources
PHAROS  Q9UJW3
Protein Feature View
  • Reference Sequence

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
CpApG DNA (25-MER)E, F25Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A, D
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.845α = 90
b = 193.845β = 90
c = 49.884γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-09-06 
  • Released Date: 2020-06-10 
  • Deposition Author(s): Gao, L., Song, J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States1R35GM119721

Revision History 

  • Version 1.0: 2020-06-10
    Type: Initial release