OCA Atlas for 6NQA

6NQA

Structural Protein Transferase Dna

date

Jan 19, 2019

title

Active State Dot1l Bound To The H2b-Ubiquitinated Nucleosome Complex

authors

E.J.Worden, N.A.Hoffmann, C.Wolberger

compound

source

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_vector_type: Plasmid
Expression_system_plasmid: Pst55-16x601

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

Molecule: Histone H4
Chain: F, B
Engineered: 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: Pet3a

Molecule: Histone H2a Type 1
Chain: G, C
Engineered: Yes
Mutation: Yes

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

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dot1l, Kiaa1814, Kmt4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet32a

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Histone H3.2
Chain: E, A
Engineered: Yes
Mutation: Yes

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 Microscopy

resolution

3.54 Å

ligand

NLE, SAM

enzyme

Transferase E.C.2.1.1.43 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A, E
C, G
F, B
H, D
K

Primary reference

Mechanism 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] (313 Kb) [Save to disk]

Biological Unit Coordinates (6nqa.pdb1.gz) 307 Kb

LPC: Ligand-Protein Contacts for 6NQA

CSU: Contacts of Structural Units for 6NQA

Retrieve 6NQA in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 6NQA from S2C, [Save to disk]

View 6NQA 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 6NQA

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [6nqa_D] [6nqa_G] [6nqa_K] [6nqa_I] [6nqa_B] [6nqa_H] [6nqa_F] [6nqa_C] [6nqa_J] [6nqa_A] [6nqa_E] [6nqa_L]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 6NQA

Community annotation for 6NQA at PDBWiki (http://pdbwiki.org)

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