6EDB

Crystal structure of SRY.hcGAS-21bp dsDNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1073/pnas.1905013116
  • Primary Citation of 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 ...

    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; xiew@mskcc.org pateld@mskcc.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sex-determining region Y protein,Cyclic GMP-AMP synthaseA, B455Homo sapiensMutation(s): 0 
Gene Names: SRYTDFCGASC6orf150MB21D1
EC: 2.7.7.86
Find proteins for Q8N884 (Homo sapiens)
Explore Q8N884 
Go to UniProtKB:  Q8N884
NIH Common Fund Data Resources
PHAROS:  Q8N884
Find proteins for Q05066 (Homo sapiens)
Explore Q05066 
Go to UniProtKB:  Q05066
NIH Common Fund Data Resources
PHAROS:  Q05066
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*GP*AP*TP*CP*CP*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*G)-3')C22Homo sapiens
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*CP*GP*GP*AP*TP*C)-3')D22Homo sapiens
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.260 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.307α = 90
b = 115.827β = 90
c = 159.077γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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