7EA8

Human SETD2 bound to a nucleosome containing oncohistone mutations


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations.

Liu, Y.Zhang, Y.Xue, H.Cao, M.Bai, G.Mu, Z.Yao, Y.Sun, S.Fang, D.Huang, J.

(2021) Cell Discov 7: 32-32

  • DOI: 10.1038/s41421-021-00261-6
  • Primary Citation of Related Structures:  
    7EA5, 7EA8

  • PubMed Abstract: 
  • Substitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors. To investigate how the oncohistone mutation affects the function of SETD2 at the nucleosome level, we determined the cryo-EM structure of human SETD2 associated with an H3 ...

    Substitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors. To investigate how the oncohistone mutation affects the function of SETD2 at the nucleosome level, we determined the cryo-EM structure of human SETD2 associated with an H3.3K36M nucleosome and cofactor S-adenosylmethionine (SAM), and revealed that SETD2 is attached to the N-terminal region of histone H3 and the nucleosome DNA at superhelix location 1, accompanied with the partial unwrapping of nucleosome DNA to expose the SETD2-binding site. These structural features were also observed in the previous cryo-EM structure of the fungal Set2-nucleosome complex. By contrast with the stable association of SETD2 with the H3.3K36M nucleosome, the EM densities of SETD2 could not be observed on the wild-type nucleosome surface, suggesting that the association of SETD2 with wild-type nucleosome might be transient. The linker histone H1, which stabilizes the wrapping of nucleosome DNA at the entry/exit sites, exhibits an inhibitory effect on the activities of SETD2 and displays inversely correlated genome distributions with that of the H3K36me3 marks. Cryo-EM analysis of yeast H3K36 methyltransferase Set2 complexed with nucleosomes further revealed evolutionarily conserved structural features for nucleosome recognition in eukaryotes, and provides insights into the mechanism of activity regulation. These findings have advanced our understanding of the structural basis for the tumorigenesis mechanism of the H3.3K36M mutation and highlight the effect of nucleosome conformation on the regulation of histone modification.


    Organizational Affiliation

    School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. huangjing@shsmu.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SETD2A [auth L]245Homo sapiensMutation(s): 0 
Gene Names: SETD2HIF1HYPBKIAA1732KMT3ASET2HSPC069
EC: 2.1.1.359 (PDB Primary Data), 2.1.1 (PDB Primary Data)
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Find proteins for Q9BYW2 (Homo sapiens)
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PHAROS:  Q9BYW2
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UniProt GroupQ9BYW2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.3B [auth A],
F [auth E]
101Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6PI79 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4C [auth B],
G [auth F]
78Homo sapiensMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-DD [auth C],
H [auth G]
104Homo sapiensMutation(s): 0 
Gene Names: H2AC7H2AFGHIST1H2AD
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Find proteins for P20671 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 2-EE [auth D],
I [auth H]
125Homo sapiensMutation(s): 0 
Gene Names: H2BC21H2BFQHIST2H2BEH2BC11H2BFRHIST1H2BJ
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Entity ID: 6
MoleculeChainsLengthOrganismImage
601-DNAJ [auth I]122synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
601-DNAK [auth J]122synthetic construct
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
O [auth L]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
L,
M [auth L],
N [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-03-06 
  • Released Date: 2021-07-14 
  • Deposition Author(s): Jing, H., Liu, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32022036
National Natural Science Foundation of China (NSFC)China31570766
National Natural Science Foundation of China (NSFC)ChinaU1632130

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 2.0: 2021-07-28
    Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary