5JLB | pdb_00005jlb

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

• PDB DOI: https://doi.org/10.2210/pdb5JLB/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.190 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

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

• PubMed: 27474439 
• DOI: https://doi.org/10.1101/gad.284323.116
• Primary Citation Related Structures: 
  5JJY, 5JLB, 5JLE


• 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 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.

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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;
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;
Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York 10065, USA;
Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China;
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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.52 kDa 
• Atom Count: 2,482 
• Modeled Residue Count: 262 
• Deposited Residue Count: 293 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETD2	A	279	Homo sapiens	Mutation(s): 0  Gene Names: SETD2 EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt), 2.1.1.359 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYW2 (Homo sapiens) Explore Q9BYW2  Go to UniProtKB:  Q9BYW2
PHAROS:  Q9BYW2 GTEx:  ENSG00000181555

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	B	14	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
PHAROS:  P84243 GTEx:  ENSG00000132475 ENSG00000163041

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	I [auth A], J [auth A], K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SCN	D [auth A], E [auth A], F [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.190 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.593	α = 90
b = 76.844	β = 90
c = 77.264	γ = 90

Software Package:

Software Name	Purpose
DENZO	data collection
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description