6U90

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

  • 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 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3BA, D291Homo sapiensMutation(s): 1 
Gene Names: DNMT3B
EC: 2.1.1.37
Find proteins for Q9UBC3 (Homo sapiens)
Explore Q9UBC3 
Go to UniProtKB:  Q9UBC3
NIH Common Fund Data Resources
PHAROS:  Q9UBC3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 3-likeB, C209Homo sapiensMutation(s): 0 
Gene Names: DNMT3L
Find proteins for Q9UJW3 (Homo sapiens)
Explore Q9UJW3 
Go to UniProtKB:  Q9UJW3
NIH Common Fund Data Resources
PHAROS:  Q9UJW3
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
CpGpT DNA (25-MER)E, F25Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
H [auth A], J [auth D]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A], I [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.506α = 90
b = 191.506β = 90
c = 49.597γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
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  (Full details and data files)

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