5CFM

Crystal structure of anemone STING (Nematostella vectensis) in complex with 3', 3' cGAMP, c[G(3', 5')pA(3', 5')p]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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This is version 1.4 of the entry. See complete history


Literature

Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2',3' cGAMP Signaling.

Kranzusch, P.J.Wilson, S.C.Lee, A.S.Berger, J.M.Doudna, J.A.Vance, R.E.

(2015) Mol Cell 59: 891-903

  • DOI: 10.1016/j.molcel.2015.07.022
  • Primary Citation of Related Structures:  
    5CFL, 5CFM, 5CFN, 5CFO, 5CFP, 5CFQ, 5CFR

  • PubMed Abstract: 
  • In humans, the cGAS-STING immunity pathway signals in response to cytosolic DNA via 2',3' cGAMP, a cyclic dinucleotide (CDN) second messenger containing mixed 2'-5' and 3'-5' phosphodiester bonds. Prokaryotes also produce CDNs, but these are exclusively 3' linked, and thus the evolutionary origins of human 2',3' cGAMP signaling are unknown ...

    In humans, the cGAS-STING immunity pathway signals in response to cytosolic DNA via 2',3' cGAMP, a cyclic dinucleotide (CDN) second messenger containing mixed 2'-5' and 3'-5' phosphodiester bonds. Prokaryotes also produce CDNs, but these are exclusively 3' linked, and thus the evolutionary origins of human 2',3' cGAMP signaling are unknown. Here we illuminate the ancient origins of human cGAMP signaling by discovery of a functional cGAS-STING pathway in Nematostella vectensis, an anemone species >500 million years diverged from humans. Anemone cGAS appears to produce a 3',3' CDN that anemone STING recognizes through nucleobase-specific contacts not observed in human STING. Nevertheless, anemone STING binds mixed-linkage 2',3' cGAMP indistinguishably from human STING, trapping a unique structural conformation not induced by 3',3' CDNs. These results reveal that human mixed-linkage cGAMP achieves universal signaling by exploiting a deeply conserved STING conformational intermediate, providing critical insight for therapeutic targeting of the STING pathway.


    Organizational Affiliation

    Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA; Cancer Research Laboratory, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute (HHMI), University of California, Berkeley, CA 94720, USA. Electronic address: rvance@berkeley.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Stimulator of Interferon GenesA, B187Nematostella vectensisMutation(s): 0 
Gene Names: v1g246111
UniProt
Find proteins for A7SLZ2 (Nematostella vectensis)
Explore A7SLZ2 
Go to UniProtKB:  A7SLZ2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4BW (Subject of Investigation/LOI)
Query on 4BW

Download Ideal Coordinates CCD File 
C [auth A]2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one
C20 H24 N10 O13 P2
RFCBNSCSPXMEBK-INFSMZHSSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth B], G [auth B]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4BW Binding MOAD:  5CFM Kd: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.27α = 90
b = 81.27β = 90
c = 99.121γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI063302

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Database references
  • Version 1.2: 2015-09-30
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence