6J99

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 1.1 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


Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3A, E136Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mgh2ac14.Lh2ac14
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H123Xenopus laevisMutation(s): 2 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinK [auth L]76Homo sapiensMutation(s): 1 
Gene Names: RPS27AUBA80UBCEP1
UniProt & NIH Common Fund Data Resources
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PHAROS:  P62979
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specificL [auth K]416Homo sapiensMutation(s): 0 
Gene Names: DOT1LKIAA1814KMT4
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.360 (UniProt)
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (144-MER)I147synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)J147synthetic construct
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
M [auth K]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
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: 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

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Entry History & Funding Information

Deposition Data

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

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