2QRV Transferase Transferase Regulator date Jul 29, 2007
title Structure Of Dnmt3a-Dnmt3l C-Terminal Domain Complex
authors D.Jia, X.Cheng
compound source
Molecule: Dna (Cytosine-5)-Methyltransferase 3a
Chain: A, D, E, H
Fragment: Residues 623 To 908
Synonym: Dnmt3a, Dna Methyltransferase Hsaiiia, Dna Mtase Hsaiiia, M.Hsaiiia;
Ec: 2.1.1.37
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt3a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_plasmid: Pxc528

Molecule: Dna (Cytosine-5)-Methyltransferase 3-Like
Chain: B, C, F, G
Fragment: Residues 160 To 386
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnmt3l
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_plasmid: Pxc510
symmetry Space Group: H 3
R_factor 0.259 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
401.881 401.881 49.689 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.89 Å
ligand SAH enzyme Transferase E.C.2.1.1.37 BRENDA
note 2QRV (Molecule of the Month:pdb139)is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, E, H, D


F, B, C, G


Primary referenceStructure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation., Jia D, Jurkowska RZ, Zhang X, Jeltsch A, Cheng X, Nature. 2007 Sep 13;449(7159):248-51. Epub 2007 Aug 22. PMID:17713477
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (310 Kb) [Save to disk]
  • Biological Unit Coordinates (2qrv.pdb1.gz) 153 Kb
  • Biological Unit Coordinates (2qrv.pdb2.gz) 151 Kb
  • LPC: Ligand-Protein Contacts for 2QRV
  • CSU: Contacts of Structural Units for 2QRV
  • Likely Quarternary Molecular Structure file(s) for 2QRV
  • Structure Factors (930 Kb)
  • Retrieve 2QRV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2QRV from S2C, [Save to disk]
  • Re-refined 2qrv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2QRV 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 2QRV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2QRV, from MSDmotif at EBI
  • Fold representative 2qrv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2qrv_E] [2qrv_F] [2qrv_B] [2qrv_G] [2qrv_D] [2qrv_H] [2qrv] [2qrv_A] [2qrv_C]
  • SWISS-PROT database: [Q9Y6K1] [Q9UJW3]
  • Domain organization of [DNM3A_HUMAN] [DNM3L_HUMAN] by SWISSPFAM
  • Other resources with information on 2QRV
  • Community annotation for 2QRV at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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