7JO9

1:1 cGAS-nucleosome complex

• PDB DOI:  https://doi.org/10.2210/pdb7JO9/pdb
• EM Map EMD-22408: EMDB EMDataResource
• NAKB: 7JO9

• Classification: DNA Binding Protein/DNA/Transferase
• Organism(s): Homo sapiens, synthetic construct, Mus musculus
• Expression System: Escherichia coli BL21(DE3), Escherichia coli HB101
• Mutation(s): No 


• Deposited: 2020-08-06 Released: 2020-09-16 
• Deposition Author(s): Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of nucleosome-dependent cGAS inhibition.

Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q.

(2020) Science 370: 450-454

• PubMed: 32913000 
• DOI: https://doi.org/10.1126/science.abd0609
• Primary Citation of Related Structures:  
  7JO9, 7JOA


• PubMed Abstract: 
  

Cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase (cGAS) recognizes cytosolic foreign or damaged DNA to activate the innate immune response to infection, inflammatory diseases, and cancer. By contrast, cGAS reactivity against self-DNA in the nucleus is suppressed by chromatin tethering. We report a 3.3-angstrom-resolution cryo-electron microscopy structure of cGAS in complex with the nucleosome core particle. The structure reveals that cGAS uses two conserved arginines to anchor to the nucleosome acidic patch. The nucleosome-binding interface exclusively occupies the strong double-stranded DNA (dsDNA)-binding surface on cGAS and sterically prevents cGAS from oligomerizing into the functionally active 2:2 cGAS-dsDNA state. These findings provide a structural basis for how cGAS maintains an inhibited state in the nucleus and further exemplify the role of the nucleosome in regulating diverse nuclear protein functions.

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Organizational Affiliation: 

Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

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: gel filtration

Macromolecule Content

• Total Structure Weight: 243.02 kDa 
• Atom Count: 14,994 
• Modelled Residue Count: 1,415 
• Deposited Residue Count: 1,646 
• 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	136	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	103	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	366	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	synthetic construct

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1-beta
MODEL REFINEMENT	PHENIX	1.18

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Boyer, J.A., Spangler, C.J., Strauss, J.D., Cesmat, A.P., Liu, P., McGinty, R.K., Zhang, Q.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM133498
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R21CA234979

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references
• Version 1.2: 2020-11-04
  Changes: Database references