8G57

Structure of nucleosome-bound Sirtuin 6 deacetylase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the human Sirtuin 6-nucleosome complex.

Chio, U.S.Rechiche, O.Bryll, A.R.Zhu, J.Leith, E.M.Feldman, J.L.Peterson, C.L.Tan, S.Armache, J.P.

(2023) Sci Adv 9: eadf7586-eadf7586

  • DOI: https://doi.org/10.1126/sciadv.adf7586
  • Primary Citation of Related Structures:  
    8G57

  • PubMed Abstract: 

    Sirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups from histone H3 in nucleosomes, but the molecular basis for its nucleosomal substrate preference is unknown. Our cryo-electron microscopy structure of human SIRT6 in complex with the nucleosome shows that the catalytic domain of SIRT6 pries DNA from the nucleosomal entry-exit site and exposes the histone H3 N-terminal helix, while the SIRT6 zinc-binding domain binds to the histone acidic patch using an arginine anchor. In addition, SIRT6 forms an inhibitory interaction with the C-terminal tail of histone H2A. The structure provides insights into how SIRT6 can deacetylate both H3 K9 and H3 K56.


  • Organizational Affiliation

    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacylase sirtuin-6A [auth K]360Homo sapiensMutation(s): 1 
Gene Names: SIRT6SIR2L6
EC: 2.3.1 (PDB Primary Data), 2.3.1.286 (PDB Primary Data), 2.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N6T7 (Homo sapiens)
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Go to UniProtKB:  Q8N6T7
PHAROS:  Q8N6T7
GTEx:  ENSG00000077463 
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UniProt GroupQ8N6T7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3B [auth A],
F [auth E]
132Xenopus laevisMutation(s): 0 
Gene Names: LOC121398065
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4C [auth B],
G [auth F]
85Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/ED [auth C],
H [auth G]
129Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
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Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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UniProt GroupP04908
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-JE [auth D],
I [auth H]
125Homo sapiensMutation(s): 0 
Gene Names: H2BC11H2BFRHIST1H2BJ
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Find proteins for P06899 (Homo sapiens)
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PHAROS:  P06899
GTEx:  ENSG00000124635 
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA strand 1J [auth I]150synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA strand 2K [auth J]150synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9.8
MODEL REFINEMENTPHENIX1.20
RECONSTRUCTIONcryoSPARC3.32

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32GM137463
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM127034
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United StatesT32BM107000
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM127034

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection, Refinement description