6Y5D

Structure of human cGAS (K394E) bound to the nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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 mechanism of cGAS inhibition by the nucleosome.

Pathare, G.R.Decout, A.Gluck, S.Cavadini, S.Makasheva, K.Hovius, R.Kempf, G.Weiss, J.Kozicka, Z.Guey, B.Melenec, P.Fierz, B.Thoma, N.H.Ablasser, A.

(2020) Nature 587: 668-672

  • DOI: https://doi.org/10.1038/s41586-020-2750-6
  • Primary Citation of Related Structures:  
    6Y5D, 6Y5E

  • PubMed Abstract: 

    The DNA sensor cyclic GMP-AMP synthase (cGAS) initiates innate immune responses following microbial infection, cellular stress and cancer 1 . Upon activation by double-stranded DNA, cytosolic cGAS produces 2'3' cGMP-AMP, which triggers the induction of inflammatory cytokines and type I interferons  2-7 . cGAS is also present inside the cell nucleus, which is replete with genomic DNA 8 , where chromatin has been implicated in restricting its enzymatic activity 9 . However, the structural basis for inhibition of cGAS by chromatin remains unknown. Here we present the cryo-electron microscopy structure of human cGAS bound to nucleosomes. cGAS makes extensive contacts with both the acidic patch of the histone H2A-H2B heterodimer and nucleosomal DNA. The structural and complementary biochemical analysis also find cGAS engaged to a second nucleosome in trans. Mechanistically, binding of the nucleosome locks cGAS into a monomeric state, in which steric hindrance suppresses spurious activation by genomic DNA. We find that mutations to the cGAS-acidic patch interface are sufficient to abolish the inhibitory effect of nucleosomes in vitro and to unleash the activity of cGAS on genomic DNA in living cells. Our work uncovers the structural basis of the interaction between cGAS and chromatin and details a mechanism that permits self-non-self discrimination of genomic DNA by cGAS.


  • Organizational Affiliation

    Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland. andrea.ablasser@epfl.ch.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E, M, Q
98Homo sapiensMutation(s): 0 
Gene Names: HIST2H3AHIST2H3CH3F2H3FMHIST2H3D
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Find proteins for Q71DI3 (Homo sapiens)
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Go to UniProtKB:  Q71DI3
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UniProt GroupQ71DI3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F, N, R
103Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 2-A
C, G, O, S
130Homo sapiensMutation(s): 0 
Gene Names: HIST2H2AA3H2AFOHIST2H2AAHIST2H2AA4
UniProt
Find proteins for Q6FI13 (Homo sapiens)
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UniProt GroupQ6FI13
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-K
D, H, P, T
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BKH2BFTHIRIP1
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Find proteins for O60814 (Homo sapiens)
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PHAROS:  O60814
GTEx:  ENSG00000197903 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic GMP-AMP synthase
K, L
362Homo sapiensMutation(s): 0 
Gene Names: CGASC6orf150MB21D1
EC: 2.7.7.86
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Find proteins for Q8N884 (Homo sapiens)
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GTEx:  ENSG00000164430 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (153-MER)
I, U
153Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (153-MER)
J, V
153Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTD
Query on PTD

Download Ideal Coordinates CCD File 
AA [auth H]
DA [auth M]
EA [auth O]
FA [auth S]
GA [auth S]
AA [auth H],
DA [auth M],
EA [auth O],
FA [auth S],
GA [auth S],
W [auth A],
X [auth C],
Y [auth G],
Z [auth H]
PENTANEDIAL
C5 H8 O2
SXRSQZLOMIGNAQ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth K],
CA [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Switzerland666068
European Research Council (ERC)Switzerland724022
European Research Council (ERC)Switzerland804933
Swiss National Science FoundationSwitzerlandBSSGI0-155984

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references