6Y5D | pdb_00006y5d

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

Validation slider image for 6Y5D

This is version 1.2 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 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
    • Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 478.34 kDa 
  • Atom Count: 30,372 
  • Modeled Residue Count: 2,830 
  • Deposited Residue Count: 3,164 
  • Unique protein chains: 5
  • Unique nucleic acid chains: 2

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
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens)
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Go to UniProtKB:  Q71DI3
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UniProt GroupQ71DI3
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4
B, F, N, R
103Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
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UniProt GroupP62805
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Reference Sequence
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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
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Find proteins for Q6FI13 (Homo sapiens)
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PHAROS:  Q6FI13
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UniProt GroupQ6FI13
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Reference Sequence
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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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Reference Sequence
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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)
Explore Q8N884 
Go to UniProtKB:  Q8N884
PHAROS:  Q8N884
GTEx:  ENSG00000164430 
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UniProt GroupQ8N884
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (153-MER)
I, U
153Homo sapiens
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Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (153-MER)
J, V
153Homo sapiens
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Reference Sequence

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
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary