8GIR | pdb_00008gir

Structure of Ternary Complex of mouse cGAS with dsDNA and Bound ATP: with 10mM Mg2+ and 0.2mM Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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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: 108.7 kDa 
  • Atom Count: 7,443 
  • Modeled Residue Count: 776 
  • Deposited Residue Count: 800 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclic GMP-AMP synthaseA,
B [auth C]
364Mus musculusMutation(s): 0 
Gene Names: CgasMb21d1
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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8C6L5
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
Palindromic DNA18C [auth E],
D [auth F],
E [auth I],
F [auth J]
18synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
G [auth A],
K [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
H [auth A],
L [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN
(Subject of Investigation/LOI)

Query on MN



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
M [auth C],
N [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.545α = 90
b = 98.506β = 90
c = 142.009γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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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: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Database references