6F57

Crystal structure of DNMT3A-DNMT3L in complex with single CpG-containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.098 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for DNMT3A-mediated de novo DNA methylation

Zhang, Z.M.Lu, R.Wang, P.Chen, D.Gao, L.Liu, S.Ji, D.Rothbart, S.B.Wang, Y.Wang, G.G.Song, J.

(2018) Nature --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA (cytosine-5)-methyltransferase 3A
A, D
285Homo sapiensGene Names: DNMT3A
EC: 2.1.1.37
Find proteins for Q9Y6K1 (Homo sapiens)
Go to Gene View: DNMT3A
Go to UniProtKB:  Q9Y6K1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA (cytosine-5)-methyltransferase 3-like
B, C
209Homo sapiensGene Names: DNMT3L
Find proteins for Q9UJW3 (Homo sapiens)
Go to Gene View: DNMT3L
Go to UniProtKB:  Q9UJW3
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3')E,G10Homo sapiens
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3')F,H11Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, D
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
Z
Query on Z
F, H
DNA LINKINGC9 H13 N2 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.098 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 176.611α = 90.00
b = 49.559β = 90.00
c = 162.259γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
Cootmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-12-01 
  • Released Date: 2018-01-31 
  • Deposition Author(s): Zhang, Z.M., Song, J.

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-07
    Type: Database references