7C0M

Human cGAS-nucleosome complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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 basis for the inhibition of cGAS by nucleosomes.

Kujirai, T., Zierhut, C., Takizawa, Y., Kim, R., Negishi, L., Uruma, N., Hirai, S., Funabiki, H., Kurumizaka, H.

(2020) Science 

  • DOI: 10.1126/science.abd0237
  • Primary Citation of Related Structures:  
    7C0M

  • PubMed Abstract: 

    • The cyclic GMP-AMP synthase (cGAS) senses invasion of pathogenic DNA and stimulates inflammatory signaling, autophagy and apoptosis. Organization of host DNA into nucleosomes was proposed to limit cGAS autoinduction, but the underlying mechanism was ...

    The cyclic GMP-AMP synthase (cGAS) senses invasion of pathogenic DNA and stimulates inflammatory signaling, autophagy and apoptosis. Organization of host DNA into nucleosomes was proposed to limit cGAS autoinduction, but the underlying mechanism was unknown. Here, we report the structural basis for this inhibition. In the cryo-EM structure of the human cGAS-nucleosome core particle (NCP) complex, two cGAS monomers bridge two NCPs by binding the acidic patch of H2A-H2B and nucleosomal DNA. In this configuration, all three known cGAS DNA-binding sites, required for cGAS activation, are repurposed or become inaccessible, and cGAS dimerization, another prerequisite for activation, is inhibited. Mutating key residues linking cGAS and the acidic patch alleviates nucleosomal inhibition. This study establishes a structural framework for why cGAS is silenced on chromatinized self-DNA.

    Organizational Affiliation: 

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1A, E, a, e139Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
GTEx  ENSG00000197409GTEx  ENSG00000197153GTEx  ENSG00000278828GTEx  ENSG00000275714GTEx  ENSG00000273983GTEx  ENSG00000274750GTEx  ENSG00000275379GTEx  ENSG00000277775
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F, b, f106Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805
GTEx  ENSG00000274618GTEx  ENSG00000197238GTEx  ENSG00000197837GTEx  ENSG00000158406GTEx  ENSG00000278705GTEx  ENSG00000197061GTEx  ENSG00000270882GTEx  ENSG00000270276GTEx  ENSG00000273542GTEx  ENSG00000277157GTEx  ENSG00000276966GTEx  ENSG00000276180GTEx  ENSG00000278637GTEx  ENSG00000275126
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC, G, c, g133Homo sapiensMutation(s): 0 
Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
Find proteins for P04908 (Homo sapiens)
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PHAROS  P04908
GTEx  ENSG00000277075GTEx  ENSG00000278463
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JD, H, d, h129Homo sapiensMutation(s): 0 
Gene Names: H2BC11, H2BFR, HIST1H2BJ
Find proteins for P06899 (Homo sapiens)
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PHAROS  P06899
GTEx  ENSG00000124635
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclic GMP-AMP synthaseK, k380Homo sapiensMutation(s): 0 
Gene Names: CGAS, C6orf150, MB21D1
EC: 2.7.7.86
Find proteins for Q8N884 (Homo sapiens)
Explore Q8N884 
Go to UniProtKB:  Q8N884
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PHAROS  Q8N884
GTEx  ENSG00000164430
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (145-MER)I, i145synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)J, j145synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
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K, k
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP17H01408
Japan Society for the Promotion of Science (JSPS)JapanJP18H05534
Japan Society for the Promotion of Science (JSPS)JapanJP19K06522
Japan Science and TechnologyJapanJPMJCR16G1
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101076
Japan Science and TechnologyJapanJPMJER1901

Revision History 

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