6PA7 Transferase Dna date Jun 11, 2019
title The Cryo-Em Structure Of The Human Dnmt3a2-Dnmt3b3 Complex B Nucleosome.
authors T.H.Xu, M.Liu, X.E.Zhou, G.Liang, G.Zhao, H.E.Xu, K.Melcher, P.A.Jo
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a Type 1
Chain: C, G
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b 1.1
Chain: D, H
Synonym: H2b1.1
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (167-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (167-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (Cytosine-5)-Methyltransferase 3a
Chain: K, P
Synonym: Dnmt3a,Dna Methyltransferase Hsaiiia,M.Hsaiiia
Ec: 2.1.1.37
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt3a
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Dna (Cytosine-5)-Methyltransferase 3b
Chain: N, S
Synonym: Dnmt3b,Dna Methyltransferase Hsaiiib,M.Hsaiiib
Ec: 2.1.1.37
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt3b
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 2.94 Å
ligand CL, SAH enzyme Transferase E.C.2.1.1.37 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


P, K


S, N
  • DNA (cytosine-5-)-methyltran...


  • Primary referenceStructure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B., Xu TH, Liu M, Zhou XE, Liang G, Zhao G, Xu HE, Melcher K, Jones PA, Nature. 2020 Oct;586(7827):151-155. doi: 10.1038/s41586-020-2747-1. Epub 2020 Sep, 23. PMID:32968275
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (391 Kb) [Save to disk]
  • Biological Unit Coordinates (6pa7.pdb1.gz) 370 Kb
  • LPC: Ligand-Protein Contacts for 6PA7
  • CSU: Contacts of Structural Units for 6PA7
  • Retrieve 6PA7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6PA7 from S2C, [Save to disk]
  • View 6PA7 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6PA7
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6pa7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6pa7_S] [6pa7_J] [6pa7_N] [6pa7_F] [6pa7_H] [6pa7_E] [6pa7_I] [6pa7_P] [6pa7_A] [6pa7_G] [6pa7_C] [6pa7_K] [6pa7_B] [6pa7_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6PA7
  • Community annotation for 6PA7 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science