Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2EF Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer -A6B2CD 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 256400.09 
• Atom Count: 15266 
• Residue Count: 1770 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

6J99

Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome

• DOI: 10.2210/pdb6J99/pdb
• EMDataResource: EMD-9783

• Classification: TRANSCRIPTION
• Organism(s): synthetic construct, Xenopus laevis, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2019-01-22 Released: 2019-02-27 
• Deposition Author(s): Yao, T., Huang, J.
• Funding Organization(s): Ministry of Science and Technology (China); National Natural Science Foundation of China 

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.1 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural 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.

(2019) Cell Res. 29: 330-333

• PubMed: 30770869 
• DOI: 10.1038/s41422-019-0146-7

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone H3	A, E	136	Xenopus laevis	Mutation(s): 0
Find proteins for A0A310TTQ1 (Xenopus laevis) Go to UniProtKB:  A0A310TTQ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F	103	Xenopus laevis	Mutation(s): 0
Find proteins for P62799 (Xenopus laevis) Go to UniProtKB:  P62799

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A	C, G	130	Xenopus laevis	Mutation(s): 0  Gene Names: hist1h2aj (h2ac14, LOC494591)
Find proteins for Q6AZJ8 (Xenopus laevis) Go to UniProtKB:  Q6AZJ8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B 1.1	D, H	123	Xenopus laevis	Mutation(s): 2
Find proteins for P02281 (Xenopus laevis) Go to UniProtKB:  P02281

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin	L	76	Homo sapiens	Mutation(s): 1  Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens) Go to Gene View: RPS27A Go to UniProtKB:  P62979

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
Histone-lysine N-methyltransferase, H3 lysine-79 specific	K	416	Homo sapiens	Mutation(s): 0  Gene Names: DOT1L (KIAA1814, KMT4) EC: 2.1.1.43
Find proteins for Q8TEK3 (Homo sapiens) Go to Gene View: DOT1L Go to UniProtKB:  Q8TEK3

Entity ID: 5
Molecule	Chains	Length	Organism
DNA (144-MER)	I	147	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism
DNA (145-MER)	J	147	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SAH	K	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.1 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Software Package:

Software Name	Purpose
PHENIX	refinement
phenix.real_space_refine	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-01-22 
• Released Date: 2019-02-27 
• Deposition Author(s): Yao, T., Huang, J.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2016YFA0501803
National Natural Science Foundation of China	China	31570766
National Natural Science Foundation of China	China	U1632130

Revision History 

• Version 1.0: 2019-02-27
  Type: Initial release
• Version 1.1: 2019-04-10
  Type: Data collection, Database references