6J99

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3
A, E
136Xenopus laevisMutation(s): 0 
Find proteins for A0A310TTQ1 (Xenopus laevis)
Go to UniProtKB:  A0A310TTQ1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2aj (h2ac14, LOC494591)
Find proteins for Q6AZJ8 (Xenopus laevis)
Go to UniProtKB:  Q6AZJ8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
123Xenopus laevisMutation(s): 2 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
L
76Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-79 specific
K
416Homo sapiensMutation(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
MoleculeChainsLengthOrganism
DNA (144-MER)I147synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (145-MER)J147synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download 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: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references