Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B2C1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content

• Total Structure Weight: 223.09 kDa 
• Atom Count: 15,292 
• Modelled Residue Count: 1,426 
• Deposited Residue Count: 1,426 
• Unique protein chains: 8
• Unique nucleic acid chains: 2

 6Y5E

Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex)

• PDB DOI:  https://doi.org/10.2210/pdb6Y5E/pdb
• EM Map EMD-10695: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-02-25 Released: 2020-09-23 
• Deposition Author(s): Pathare, G.R., Cavadini, S., Kempf, G., Thoma, N.H.
• Funding Organization(s): Swiss National Science Foundation, European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 32911482 
• 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.

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Organizational Affiliation: 

Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	96	Homo sapiens	Mutation(s): 0  Gene Names: HIST2H3A, HIST2H3C, H3F2, H3FM, HIST2H3D, H3C15, H3C14, H3C13
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3  Go to UniProtKB:  Q71DI3
PHAROS:  Q71DI3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B	81	Homo sapiens	Mutation(s): 0  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 2-C	C	107	Homo sapiens	Mutation(s): 0  Gene Names: HIST2H2AC, H2AFQ, H2AC20
UniProt & NIH Common Fund Data Resources
Find proteins for Q16777 (Homo sapiens) Explore Q16777  Go to UniProtKB:  Q16777
PHAROS:  Q16777

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-K	D	93	Homo sapiens	Mutation(s): 0  Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens) Explore O60814  Go to UniProtKB:  O60814
PHAROS:  O60814

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	F	83	Homo sapiens	Mutation(s): 0  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 2-C	G	108	Homo sapiens	Mutation(s): 0  Gene Names: HIST2H2AC, H2AFQ, H2AC20
UniProt & NIH Common Fund Data Resources
Find proteins for Q16777 (Homo sapiens) Explore Q16777  Go to UniProtKB:  Q16777
PHAROS:  Q16777

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-K	H	94	Homo sapiens	Mutation(s): 0  Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens) Explore O60814  Go to UniProtKB:  O60814
PHAROS:  O60814

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic GMP-AMP synthase	K	362	Homo sapiens	Mutation(s): 0  Gene Names: CGAS, C6orf150, MB21D1 EC: 2.7.7.86
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N884 (Homo sapiens) Explore Q8N884  Go to UniProtKB:  Q8N884
PHAROS:  Q8N884

Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (153-MER)	I	153	Homo sapiens

Entity ID: 9
Molecule	Chains	Length	Organism	Image
DNA (153-MER)	J	153	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTD	L [auth A], M [auth C], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth H], T [auth K]	PENTANEDIAL C5 H8 O2 SXRSQZLOMIGNAQ-UHFFFAOYSA-N
ZN	S [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Pathare, G.R., Cavadini, S., Kempf, G., Thoma, N.H.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	BSSGI0-155984
European Research Council (ERC)	Switzerland	804933
European Research Council (ERC)	Switzerland	666068
European Research Council (ERC)	Switzerland	724022
Swiss National Science Foundation	Switzerland	31003A_179541

Revision History  

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