6XJD

Two mouse cGAS catalytic domain binding to human assembled nucleosome

• PDB DOI:  https://doi.org/10.2210/pdb6XJD/pdb
• NAKB: 6XJD
• EM Map EMD-22206: EMDB EMDataResource

• Classification: IMMUNE SYSTEM/DNA
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-06-23 Released: 2020-09-16 
• Deposition Author(s): Xu, P., Li, P., Zhao, B.
• Funding Organization(s): Welch Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The molecular basis of tight nuclear tethering and inactivation of cGAS.

Zhao, B., Xu, P., Rowlett, C.M., Jing, T., Shinde, O., Lei, Y., West, A.P., Liu, W.R., Li, P.

(2020) Nature 587: 673-677

• PubMed: 32911481 
• DOI: https://doi.org/10.1038/s41586-020-2749-z
• Primary Citation of Related Structures:  
  6X59, 6X5A, 6XJD


• PubMed Abstract: 
  

Nucleic acids derived from pathogens induce potent innate immune responses ^1-6 . Cyclic GMP-AMP synthase (cGAS) is a double-stranded DNA sensor that catalyses the synthesis of the cyclic dinucleotide cyclic GMP-AMP, which mediates the induction of type I interferons through the STING-TBK1-IRF3 signalling axis ^7-11 . cGAS was previously thought to not react with self DNA owing to its cytosolic localization ^2,12,13 ; however, recent studies have shown that cGAS is localized mostly in the nucleus and has low activity as a result of tight nuclear tethering ^14-18 . Here we show that cGAS binds to nucleosomes with nanomolar affinity and that nucleosome binding potently inhibits its catalytic activity. To elucidate the molecular basis of cGAS inactivation by nuclear tethering, we determined the structure of mouse cGAS bound to human nucleosome by cryo-electron microscopy. The structure shows that cGAS binds to a negatively charged acidic patch formed by histones H2A and H2B via its second DNA-binding site ¹⁹ . High-affinity nucleosome binding blocks double-stranded DNA binding and maintains cGAS in an inactive conformation. Mutations of cGAS that disrupt nucleosome binding alter cGAS-mediated signalling in cells.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B2C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 286.79 kDa 
• Atom Count: 17,957 
• Modelled Residue Count: 1,775 
• Deposited Residue Count: 2,020 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	135	Homo sapiens	Mutation(s): 0  Gene Names: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D
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, F	102	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16
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 1	C, G	129	Homo sapiens	Mutation(s): 0  Gene Names:  H2AC11, H2AFP, HIST1H2AG, H2AC13, H2AFC, HIST1H2AI, H2AC15, H2AFD, HIST1H2AK, H2AC16, H2AFI, HIST1H2AL, H2AC17, H2AFN, HIST1H2AM
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S8 (Homo sapiens) Explore P0C0S8  Go to UniProtKB:  P0C0S8
PHAROS:  P0C0S8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-C/E/F/G/I	D, H	125	Homo sapiens	Mutation(s): 0  Gene Names:  H2BC4, H2BFL, HIST1H2BC, H2BC6, H2BFH, HIST1H2BE, H2BC7, H2BFG, HIST1H2BF, H2BC8, H2BFA, HIST1H2BG, H2BC10, H2BFK, HIST1H2BI
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens) Explore P62807  Go to UniProtKB:  P62807
PHAROS:  P62807

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic GMP-AMP synthase	K, L	372	Mus musculus	Mutation(s): 0  Gene Names: Cgas, Mb21d1 EC: 2.7.7.86
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C6L5 (Mus musculus) Explore Q8C6L5  Go to UniProtKB:  Q8C6L5
IMPC:  MGI:2442261

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	I	147	Homo sapiens

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	J	147	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	M [auth K], N [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0b

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Xu, P., Li, P., Zhao, B.

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Funding Organization	Location	Grant Number
Welch Foundation	United States	Grant A-1931-20170325
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Grant R01 AI145287

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references, Structure summary
• Version 1.2: 2020-12-09
  Changes: Database references