6J99 Transcription date Jan 22, 2019
title Cryo-Em Structure Of Human Dot1l In Complex With An H2b- Monoubiquitinated Nucleosome
authors T.Yao, J.Huang
compound source
Molecule: Histone H3
Chain: A, E
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Xelaev_18002543mg
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
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
Expression_system_taxid: 562

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

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

Molecule: Dna (144-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (145-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Ubiquitin
Chain: L
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rps27a, Uba80, Ubcep1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone-Lysine N-Methyltransferase, H3 Lysine-79
Chain: K
Synonym: Dot1-Like Protein,Histone H3-K79 Methyltransferase Hmtase,Lysine N-Methyltransferase 4;
Ec: 2.1.1.43
Engineered: Yes
Other_details: S-Adenosyl-L-Homocysteine

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dot1l, Kiaa1814, Kmt4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
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 4.10 Å
ligand SAH enzyme Transferase E.C.2.1.1.43 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


K


Primary referenceStructural basis of the crosstalk between histone H2B monoubiquitination and H3 lysine 79 methylation on nucleosome., Yao T, Jing W, Hu Z, Tan M, Cao M, Wang Q, Li Y, Yuan G, Lei M, Huang J, Cell Res. 2019 Feb 15. pii: 10.1038/s41422-019-0146-7. doi:, 10.1038/s41422-019-0146-7. PMID:30770869
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (312 Kb) [Save to disk]
  • Biological Unit Coordinates (6j99.pdb1.gz) 306 Kb
  • LPC: Ligand-Protein Contacts for 6J99
  • CSU: Contacts of Structural Units for 6J99
  • Retrieve 6J99 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6J99 from S2C, [Save to disk]
  • View 6J99 in 3D
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6J99
  • 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 6j99 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6j99_H] [6j99_J] [6j99_C] [6j99_G] [6j99_E] [6j99_D] [6j99_F] [6j99_L] [6j99_B] [6j99_K] [6j99_A] [6j99_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6J99
  • Community annotation for 6J99 at PDBWiki (http://pdbwiki.org)

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