5JLB

Crystal structure of SETD2 bound to histone H3.3 K36I peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis for oncohistone H3 recognition by SETD2 methyltransferase

Yang, S.Zheng, X.Lu, C.Li, G.M.Allis, C.D.Li, H.

(2016) Genes Dev 30: 1611-1616

  • DOI: 10.1101/gad.284323.116
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • High-frequency point mutations of genes encoding histones have been identified recently as novel drivers in a number of tumors. Specifically, the H3K36M/I mutations were shown to be oncogenic in chondroblastomas and undifferentiated sarcomas by inhib ...

    High-frequency point mutations of genes encoding histones have been identified recently as novel drivers in a number of tumors. Specifically, the H3K36M/I mutations were shown to be oncogenic in chondroblastomas and undifferentiated sarcomas by inhibiting H3K36 methyltransferases, including SETD2. Here we report the crystal structures of the SETD2 catalytic domain bound to H3K36M or H3K36I peptides with SAH (S-adenosylhomocysteine). In the complex structure, the catalytic domain adopts an open conformation, with the K36M/I peptide snuggly positioned in a newly formed substrate channel. Our structural and biochemical data reveal the molecular basis underying oncohistone recognition by and inhibition of SETD2.


    Organizational Affiliation

    MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase SETD2
A
279Homo sapiensMutation(s): 0 
Gene Names: SETD2HIF1HYPBKIAA1732KMT3ASET2HSPC069
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.359 (UniProt), 2.1.1 (UniProt)
Find proteins for Q9BYW2 (Homo sapiens)
Go to UniProtKB:  Q9BYW2
NIH Common Fund Data Resources
PHAROS  Q9BYW2
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
B
14Homo sapiensMutation(s): 1 
Gene Names: H3-3AH3.3AH3F3H3F3APP781H3-3BH3.3BH3F3B
Find proteins for P84243 (Homo sapiens)
Go to UniProtKB:  P84243
NIH Common Fund Data Resources
PHAROS  P84243
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.593α = 90
b = 76.844β = 90
c = 77.264γ = 90
Software Package:
Software NamePurpose
DENZOdata collection
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-04-26 
  • Released Date: 2016-11-02 
  • Deposition Author(s): Li, H., Yang, S.

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection, Database references, Derived calculations