PDBsum entry 6y5d

Immune system

PDB id: 6y5d

Contents

Protein chains

96 a.a.

81 a.a.

107 a.a.

93 a.a.

362 a.a.

77 a.a.

DNA/RNA

Ligands

PTD ×9

Metals

_ZN ×2

PDB id:

6y5d

Name:

Immune system

Title:

Structure of human cgas (k394e) bound to the nucleosome

Structure:

Histone h3.2. Chain: a, e, m, q. Synonym: histone h3/m,histone h3/o. Engineered: yes. Histone h4. Chain: b, f, n, r. Engineered: yes. Histone h2a type 2-a. Chain: c, g, o, s.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hist2h3a, hist2h3c, h3f2, h3fm, hist2h3d. Expressed in: escherichia coli k-12. Expression_system_taxid: 83333. Gene: 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,

Authors:

G.R.Pathare,S.Cavadini,G.Kempf,N.H.Thoma

Key ref:

G.R.Pathare et al. (2020). Structural mechanism of cGAS inhibition by the nucleosome. Nature, 587, 668-672. PubMed id: 32911482 DOI: 10.1038/s41586-020-2750-6

Date:

25-Feb-20 Release date: 23-Sep-20

Protein chains

Q71DI3  (H32_HUMAN) -  Histone H3.2 from Homo sapiens

Seq: 136 a.a.

Struc: 96 a.a.*

Protein chains

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 81 a.a.

Protein chains

Q6FI13  (H2A2A_HUMAN) -  Histone H2A type 2-A from Homo sapiens

Seq: 130 a.a.

Struc: 107 a.a.

Protein chains

O60814  (H2B1K_HUMAN) -  Histone H2B type 1-K from Homo sapiens

Seq: 126 a.a.

Struc: 93 a.a.

Protein chains

Q8N884  (CGAS_HUMAN) -  Cyclic GMP-AMP synthase from Homo sapiens

Seq: 522 a.a.

Struc: 362 a.a.*

Protein chain

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 77 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

A-T-C-C-T-G-G-A-G-A-A-T-C-C-C-G-G-T-G-C-C-G-A-G-G-C-C-G-C-T-C-A-A-T-T-G-G-T-C- 153 bases

A-T-C-A-C-A-G-G-A-T-G-T-A-T-A-T-A-T-C-T-G-A-C-A-C-G-T-G-C-C-T-G-G-A-G-A-C-T-A- 153 bases

A-T-C-C-T-G-G-A-G-A-A-T-C-C-C-G-G-T-G-C-C-G-A-G-G-C-C-G-C-T-C-A-A-T-T-G-G-T-C- 153 bases

A-T-C-A-C-A-G-G-A-T-G-T-A-T-A-T-A-T-C-T-G-A-C-A-C-G-T-G-C-C-T-G-G-A-G-A-C-T-A- 153 bases

Enzyme reactions

• Enzyme class: Chains K, L: E.C.2.7.7.86 - cyclic GMP-AMP synthase.
• Reaction: GTP + ATP = 2',3'-cGAMP + 2 diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/s41586-020-2750-6

Nature 587:668-672 (2020)

PubMed id: 32911482

Structural mechanism of cGAS inhibition by the nucleosome.

G.R.Pathare, A.Decout, S.Glück, S.Cavadini, K.Makasheva, R.Hovius, G.Kempf, J.Weiss, Z.Kozicka, B.Guey, P.Melenec, B.Fierz, N.H.Thomä, A.Ablasser.

ABSTRACT

The DNA sensor cyclic GMP-AMP synthase (cGAS) initiates innate immune responses following microbial infection, cellular stress and cancer¹. 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 DNA⁸, where chromatin has been implicated in restricting its enzymatic activity⁹. 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.