6EDC | pdb_00006edc

hcGAS-16bp dsDNA complex

• PDB DOI: https://doi.org/10.2210/pdb6EDC/pdb
• NAKB: 6EDC

• Classification: Transferase/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-08-09 Released: 2019-05-29 
• Deposition Author(s): Xie, W., Lama, L., Adura, C., Glickman, J.F., Tuschl, T., Patel, D.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.278 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Human cGAS catalytic domain has an additional DNA-binding interface that enhances enzymatic activity and liquid-phase condensation.

Xie, W., Lama, L., Adura, C., Tomita, D., Glickman, J.F., Tuschl, T., Patel, D.J.

(2019) Proc Natl Acad Sci U S A 116: 11946-11955

• PubMed: 31142647 
• DOI: https://doi.org/10.1073/pnas.1905013116
• Primary Citation Related Structures: 
  6EDB, 6EDC, 6O47


• PubMed Abstract: 
  

  The cyclic GMP-AMP synthase (cGAS)-cGAMP-STING pathway plays a key role in innate immunity, with cGAS sensing both pathogenic and mislocalized DNA in the cytoplasm. Human cGAS (h-cGAS) constitutes an important drug target for control of antiinflammatory responses that can contribute to the onset of autoimmune diseases. Recent studies have established that the positively charged N-terminal segment of cGAS contributes to enhancement of cGAS enzymatic activity as a result of DNA-induced liquid-phase condensation. We have identified an additional cGAS ^CD -DNA interface (labeled site-C; CD, catalytic domain) in the crystal structure of a human SRY.cGAS ^CD -DNA complex, with mutations along this basic site-C cGAS interface disrupting liquid-phase condensation, as monitored by cGAMP formation, gel shift, spin-down, and turbidity assays, as well as time-lapse imaging of liquid droplet formation. We expand on an earlier ladder model of cGAS dimers bound to a pair of parallel-aligned DNAs to propose a multivalent interaction-mediated cluster model to account for DNA-mediated condensation involving both the N-terminal domain of cGAS and the site-C cGAS-DNA interface. We also report the crystal structure of the h-cGAS ^CD -DNA complex containing a triple mutant that disrupts the site-C interface, with this complex serving as a future platform for guiding cGAS inhibitor development at the DNA-bound h-cGAS level. Finally, we solved the structure of RU.521 bound in two alternate alignments to apo h-cGAS ^CD , thereby occupying more of the catalytic pocket and providing insights into further optimization of active-site-binding inhibitors.

---

Organizational Affiliation: 
• Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065; [e-mail] [e-mail].
Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY 10065.
High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY 10065.
Tri-Institutional Therapeutics Discovery Institute, New York, NY 10021.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.15 kDa 
• Atom Count: 3,499 
• Modeled Residue Count: 379 
• Deposited Residue Count: 400 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic GMP-AMP synthase	A	366	Homo sapiens	Mutation(s): 3  Gene Names: CGAS, C6orf150, MB21D1 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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*AP*A)-3')	B	17	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*T)-3')	C	17	Homo sapiens

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.278 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.813	α = 90
b = 99.813	β = 90
c = 238.644	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): Xie, W., Lama, L., Adura, C., Glickman, J.F., Tuschl, T., Patel, D.J.

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Database references
• Version 1.2: 2019-06-26
  Changes: Data collection, Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description