8SI0 | pdb_00008si0

Structure of binary complex of human cGAS and bound cGAMP

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2023-04-14 Released: 2024-04-24 
  • Deposition Author(s): Wu, S., Sohn, J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.280 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8SI0

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS.

Wu, S.Gabelli, S.B.Sohn, J.

(2024) Nat Commun 15: 4012-4012

  • DOI: https://doi.org/10.1038/s41467-024-48365-3
  • Primary Citation Related Structures: 
    8EAE, 8G10, 8G1J, 8G23, 8GIM, 8GIN, 8GIO, 8GIP, 8GIR, 8GIS, 8GIT, 8SHK, 8SHU, 8SHY, 8SHZ, 8SI0, 8SJ0, 8SJ1, 8SJ2, 8SJ8, 8SKT

  • PubMed Abstract: 

    cGAS activates innate immune responses against cytosolic double-stranded DNA. Here, by determining crystal structures of cGAS at various reaction stages, we report a unifying catalytic mechanism. apo-cGAS assumes an array of inactive conformations and binds NTPs nonproductively. Dimerization-coupled double-stranded DNA-binding then affixes the active site into a rigid lock for productive metal•substrate binding. A web-like network of protein•NTP, intra-NTP, and inter-NTP interactions ensures the stepwise synthesis of 2'-5'/3'-5'-linked cGAMP while discriminating against noncognate NTPs and off-pathway intermediates. One divalent metal is sufficient for productive substrate binding, and capturing the second divalent metal is tightly coupled to nucleotide and linkage specificities, a process which manganese is preferred over magnesium by 100-fold. Additionally, we elucidate how mouse cGAS achieves more stringent NTP and linkage specificities than human cGAS. Together, our results reveal that an adaptable, yet precise lock-and-key-like mechanism underpins cGAS catalysis.


  • Organizational Affiliation
    • Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Macromolecule Content 

  • Total Structure Weight: 43.71 kDa 
  • Atom Count: 2,834 
  • Modeled Residue Count: 339 
  • Deposited Residue Count: 369 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclic GMP-AMP synthase369Homo sapiensMutation(s): 0 
Gene Names: CGASC6orf150MB21D1
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
GTEx:  ENSG00000164430 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N884
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.280 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.927α = 90
b = 59.657β = 90
c = 125.327γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Database references