6J99 | pdb_00006j99

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

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1038/s41422-019-0146-7
  • Primary Citation of Related Structures:  
    6J99
    • Organizational Affiliation: 
    • State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 201210, China.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3
A, E
136Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis)
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UniProt GroupA0A310TTQ1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
123Xenopus laevisMutation(s): 2 
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinK [auth L]76Homo sapiensMutation(s): 1 
Gene Names: RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens)
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PHAROS:  P62979
GTEx:  ENSG00000143947 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specificL [auth K]416Homo sapiensMutation(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)
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PHAROS:  Q8TEK3
GTEx:  ENSG00000104885 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (144-MER)147synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-MER)147synthetic construct
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download Ideal Coordinates CCD File 
M [auth K]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Binding Affinity Annotations 
IDSourceBinding 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: 140, max: 600 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

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

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0501803
National Natural Science Foundation of ChinaChina31570766
National Natural Science Foundation of ChinaChinaU1632130

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2025-09-17
    Changes: Advisory, Data collection, Derived calculations