Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A7B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 256.40 kDa 
• Atom Count: 15266 
• Modelled Residue Count: 1452 
• Deposited 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): Xenopus laevis, synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 4.10 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
• Primary Citation of Related Structures:  
  6J99

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, E	136	Xenopus laevis	Mutation(s): 0  Gene Names: XELAEV_18002543mg
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis) Explore A0A310TTQ1  Go to UniProtKB:  A0A310TTQ1

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	130	Xenopus laevis	Mutation(s): 0  Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg, h2ac14.L, h2ac14
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8  Go to UniProtKB:  Q6AZJ8

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

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	K [auth L]	76	Homo sapiens	Mutation(s): 1  Gene Names: RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens) Explore P62979  Go to UniProtKB:  P62979
PHAROS:  P62979 GTEx:  ENSG00000143947

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase, H3 lysine-79 specific	L [auth K]	416	Homo sapiens	Mutation(s): 0  Gene Names: DOT1L, KIAA1814, KMT4 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.360 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEK3 (Homo sapiens) Explore Q8TEK3  Go to UniProtKB:  Q8TEK3
PHAROS:  Q8TEK3 GTEx:  ENSG00000104885

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	M [auth K]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	BindingDB:  6J99	Ki: min: 160, max: 270 (nM) from 2 assay(s)
		Kd: min: 150, max: 360 (nM) from 2 assay(s)
		IC50: min: 220, max: 600 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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
  Changes: Data collection, Database references