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 H3 A, E136Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
Find proteins for A0A310TTQ1 (Xenopus laevis)
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Go to UniProtKB:  A0A310TTQ1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4 B, F103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A C, G130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg, h2ac14.L, h2ac14
Find proteins for Q6AZJ8 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1 D, H123Xenopus laevisMutation(s): 2 
Find proteins for P02281 (Xenopus laevis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin L76Homo sapiensMutation(s): 1 
Gene Names: RPS27A, UBA80, UBCEP1
Find proteins for P62979 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS:  P62979
GTEx:  ENSG00000143947
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specific K416Homo sapiensMutation(s): 0 
Gene Names: DOT1L, KIAA1814, KMT4
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.360 (UniProt)
Find proteins for Q8TEK3 (Homo sapiens)
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PHAROS:  Q8TEK3
GTEx:  ENSG00000104885
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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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download Ideal Coordinates CCD File 
K
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N		 Ligand Interaction
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 

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