6JM9 Gene Regulation date Mar 07, 2019
title Cryo-Em Structure Of Dot1l Bound To Unmodified Nucleosome
authors S.Jang, J.J.Song
compound source
Molecule: Dna Strand I
Chain: I
Engineered: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli Dh5[Alpha]
Expression_system_taxid: 668369
Expression_system_strain: Dh5[Alpha]

Molecule: Dna Strand J
Chain: J
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli Dh5[Alpha]
Expression_system_taxid: 668369
Expression_system_strain: Dh5[Alpha]

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 Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Hist1h2aj, Loc494591, Xelaev_18003602mg
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21

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 Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21

Molecule: Histone-Lysine N-Methyltransferase, H3 Lysine-79
Chain: X
Synonym: Dot1-Like Protein
Ec: 2.1.1.43
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dot1l
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
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 7.30 Å
ligand SAM enzyme Transferase E.C.2.1.1.43 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


X


Primary referenceStructural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase., Jang S, Kang C, Yang HS, Jung T, Hebert H, Chung KY, Kim SJ, Hohng S, Song JJ, Genes Dev. 2019 Mar 28. pii: gad.323790.118. doi: 10.1101/gad.323790.118. PMID:30923167
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (274 Kb) [Save to disk]
  • Biological Unit Coordinates (6jm9.pdb1.gz) 269 Kb
  • LPC: Ligand-Protein Contacts for 6JM9
  • CSU: Contacts of Structural Units for 6JM9
  • Retrieve 6JM9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6JM9 from S2C, [Save to disk]
  • View 6JM9 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 6JM9
  • 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 6jm9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6jm9_D] [6jm9_H] [6jm9_C] [6jm9_G] [6jm9_A] [6jm9_X] [6jm9_J] [6jm9_B] [6jm9_E] [6jm9_F] [6jm9_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6JM9
  • Community annotation for 6JM9 at PDBWiki (http://pdbwiki.org)

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