6A5N Gene Regulation Dna date Jun 24, 2018
title Crystal Structure Of Arabidopsis Thaliana Suvh6 In Complex W Methylated Dna
authors X.Li, J.Du
compound source
Molecule: Histone-Lysine N-Methyltransferase, H3 Lysine-9 S Suvh6;
Chain: A
Synonym: Histone H3-K9 Methyltransferase 6,H3-K9-Hmtase 6,P Domain Group 23,Suppressor Of Variegation 3-9 Homolog Prote Su(Var)3-9 Homolog Protein 6;
Ec: 2.1.1.43
Engineered: Yes
Mutation: Yes
Organism_scientific: Arabidopsis Thaliana
Organism_common: Mouse-Ear Cress
Organism_taxid: 3702
Gene: Suvh6, Sdg23, Set23, At2g22740, T9i22.18
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Sumo

Molecule: Dna (5'-D(Gpapgptpapcptp(5cm)Papgpcpa 3');
Chain: C
Engineered: Yes
Other_details: Methylated Dna

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Cpapcptpgpcptpgpapgptpapcp
Chain: D
Engineered: Yes
Other_details: Complementary Dna

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.230 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.137 79.443 107.845 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 5CM, ZN enzyme Transferase E.C.2.1.1.43 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation., Li X, Harris CJ, Zhong Z, Chen W, Liu R, Jia B, Wang Z, Li S, Jacobsen SE, Du J, Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):E8793-E8802. doi:, 10.1073/pnas.1809841115. Epub 2018 Aug 27. PMID:30150382
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (198 Kb) [Save to disk]
  • Biological Unit Coordinates (6a5n.pdb1.gz) 192 Kb
  • LPC: Ligand-Protein Contacts for 6A5N
  • CSU: Contacts of Structural Units for 6A5N
  • Structure Factors (358 Kb)
  • Retrieve 6A5N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6A5N from S2C, [Save to disk]
  • View 6A5N 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 6A5N
  • 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 6a5n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6a5n_D] [6a5n_C] [6a5n_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6A5N
  • Community annotation for 6A5N at PDBWiki (http://pdbwiki.org)

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