4EMT

Crystal Structure of human STING bound to c-di-GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of STING bound to cyclic di-GMP reveals the mechanism of cyclic dinucleotide recognition by the immune system.

Shu, C.Yi, G.Watts, T.Kao, C.C.Li, P.

(2012) Nat.Struct.Mol.Biol. 19: 722-724

  • DOI: 10.1038/nsmb.2331
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • STING (stimulator of interferon genes) is an innate immune sensor of cyclic dinucleotides that regulates the induction of type I interferons. STING's C-terminal domain forms a V-shaped dimer and binds a cyclic diguanylate monophosphate (c-di-GMP) at ...

    STING (stimulator of interferon genes) is an innate immune sensor of cyclic dinucleotides that regulates the induction of type I interferons. STING's C-terminal domain forms a V-shaped dimer and binds a cyclic diguanylate monophosphate (c-di-GMP) at the dimer interface by both direct and solvent-mediated hydrogen bonds. Guanines of c-di-GMP stack against the phenolic rings of a conserved tyrosine, and mutations at the c-di-GMP binding surface reduce nucleotide binding and affect signaling.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transmembrane protein 173
A, B
188Homo sapiensMutation(s): 0 
Gene Names: TMEM173 (ERIS, MITA, STING)
Find proteins for Q86WV6 (Homo sapiens)
Go to Gene View: TMEM173
Go to UniProtKB:  Q86WV6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E

Download SDF File 
Download CCD File 
A
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
c-di-GMP; Cyclic diguanosine monophosphate
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C2EKd: 4630 nM BINDINGMOAD
C2EKd: 5000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 69.797α = 90.00
b = 78.215β = 90.00
c = 128.222γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-04-12 
  • Released Date: 2012-06-13 
  • Deposition Author(s): Li, P.

Revision History 

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-07-11
    Type: Database references
  • Version 1.2: 2012-07-25
    Type: Database references