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URL: https://www.rcsb.org/structure/4LOH

⇱ RCSB PDB - 4LOH: Crystal structure of hSTING(H232) in complex with c[G(2',5')pA(3',5')p]

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Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

 4LOH | pdb_00004loh

Crystal structure of hSTING(H232) in complex with c[G(2',5')pA(3',5')p]

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.215 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Structure-Function Analysis of STING Activation by c[G(2',5')pA(3',5')p] and Targeting by Antiviral DMXAA.

Gao, P., Ascano, M., Zillinger, T., Wang, W., Dai, P., Serganov, A.A., Gaffney, B.L., Shuman, S., Jones, R.A., Deng, L., Hartmann, G., Barchet, W., Tuschl, T., Patel, D.J.

(2013) Cell 154: 748-762

  • DOI: https://doi.org/10.1016/j.cell.2013.07.023
  • Primary Citation Related Structures: 
    4LOH, 4LOI, 4LOJ, 4LOK, 4LOL

  • PubMed Abstract: 

    Binding of dsDNA by cyclic GMP-AMP (cGAMP) synthase (cGAS) triggers formation of the metazoan second messenger c[G(2',5')pA(3',5')p], which binds the signaling protein STING with subsequent activation of the interferon (IFN) pathway. We show that human hSTING(H232) adopts a "closed" conformation upon binding c[G(2',5')pA(3',5')p] and its linkage isomer c[G(2',5')pA(2',5')p], as does mouse mSting(R231) on binding c[G(2',5')pA(3',5')p], c[G(3',5')pA(3',5')p] and the antiviral agent DMXAA, leading to similar "closed" conformations. Comparing hSTING to mSting, 2',5'-linkage-containing cGAMP isomers were more specific triggers of the IFN pathway compared to the all-3',5'-linkage isomer. Guided by structural information, we identified a unique point mutation (S162A) placed within the cyclic-dinucleotide-binding site of hSTING that rendered it sensitive to the otherwise mouse-specific drug DMXAA, a conclusion validated by binding studies. Our structural and functional analysis highlights the unexpected versatility of STING in the recognition of natural and synthetic ligands within a small-molecule pocket created by the dimerization of STING.

    • Organizational Affiliation: 
    • Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

Macromolecule Content 

  • Total Structure Weight: 43.72 kDa 
  • Atom Count: 3,173 
  • Modeled Residue Count: 368 
  • Deposited Residue Count: 376 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Stimulator of interferon genes protein
A, B
188Homo sapiensMutation(s): 0 
Gene Names: TMEM173, ERIS, MITA, STING
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UniProt & NIH Common Fund Data Resources
Find proteins for Q86WV6 (Homo sapiens)
Explore Q86WV6 
Go to UniProtKB:  Q86WV6
PHAROS:  Q86WV6
GTEx:  ENSG00000184584 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86WV6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1SY

Query on 1SY


Download:Ideal Coordinates CCD File
C [auth A]cGAMP
C20 H24 N10 O13 P2
XRILCFTWUCUKJR-INFSMZHSSA-N		👁 Image

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.215 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.5α = 83.98
b = 59.209β = 85.83
c = 59.205γ = 85.87
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references
  • Version 1.2: 2015-08-05
    Changes: Non-polymer description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.