6NJ9 Structural Protein Transferase Dna date Jan 02, 2019
title Active State Dot1l Bound To The H2b-Ubiquitinated Nucleosome Complex
authors E.J.Worden, N.A.Hoffmann, C.Wolberger
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Mutation: 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: Rosetta2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

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: Rosetta2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Histone H2a Type 1
Chain: C, G
Engineered: Yes
Mutation: 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: Rosetta2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

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
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet32a

Molecule: 601 Dna Strand 1
Chain: I
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Xl1-Blue
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pst55-16x601

Molecule: 601 Dna Strand 2
Chain: J
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Xl1-Blue
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pst55-16x601

Molecule: Histone-Lysine N-Methyltransferase, H3 Lysine-79
Chain: K, M
Synonym: Dot1-Like Protein,Histone H3-K79 Methyltransferase Hmtase,Lysine N-Methyltransferase 4;
Ec: 2.1.1.360
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dot1l, Kiaa1814, Kmt4
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet32a
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 2.96 Å
ligand NLE, SAM enzyme Transferase E.C.2.1.1.360 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


K


Primary referenceMechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L., Worden EJ, Hoffmann NA, Hicks CW, Wolberger C, Cell. 2019 Feb 8. pii: S0092-8674(19)30151-5. doi: 10.1016/j.cell.2019.02.002. PMID:30765112
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (378 Kb) [Save to disk]
  • Biological Unit Coordinates (6nj9.pdb1.gz) 362 Kb
  • LPC: Ligand-Protein Contacts for 6NJ9
  • CSU: Contacts of Structural Units for 6NJ9
  • Retrieve 6NJ9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6NJ9 from S2C, [Save to disk]
  • View 6NJ9 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 6NJ9
  • 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 6nj9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6nj9_G] [6nj9_N] [6nj9_H] [6nj9_J] [6nj9_A] [6nj9_D] [6nj9_M] [6nj9_I] [6nj9_C] [6nj9_E] [6nj9_K] [6nj9_F] [6nj9_B] [6nj9_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6NJ9
  • Community annotation for 6NJ9 at PDBWiki (http://pdbwiki.org)

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