Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 27.86 kDa 
• Atom Count: 1584 
• Modelled Residue Count: 178 
• Deposited Residue Count: 242 
• Unique protein chains: 1

5BQX

Crystal structure of human STING in complex with 3'2'-cGAMP

• PDB DOI: 10.2210/pdb5BQX/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-29 Released: 2015-06-24 
• Deposition Author(s): Wu, J., Zhang, X., Chen, Z.J., Chen, C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.187 
• R-Value Observed: 0.191 

Literature

Molecular basis for the specific recognition of the metazoan cyclic GMP-AMP by the innate immune adaptor protein STING.

Shi, H., Wu, J., Chen, Z.J., Chen, C.

(2015) Proc Natl Acad Sci U S A 112: 8947-8952

• PubMed: 26150511 
• DOI: 10.1073/pnas.1507317112
• Primary Citation of Related Structures:  
  5BQX


• PubMed Abstract: 
  

Cyclic GMP-AMP containing a unique combination of mixed phosphodiester linkages (2'3'-cGAMP) is an endogenous second messenger molecule that activates the type-I IFN pathway upon binding to the homodimer of the adaptor protein STING on the surface of endoplasmic reticulum membrane. However, the preferential binding of the asymmetric ligand 2'3'-cGAMP to the symmetric dimer of STING represents a physicochemical enigma. Here we show that 2'3'-cGAMP, but not its linkage isomers, adopts an organized free-ligand conformation that resembles the STING-bound conformation and pays low entropy and enthalpy costs in converting into the active conformation. Our results demonstrate that analyses of free-ligand conformations can be as important as analyses of protein conformations in understanding protein-ligand interactions.

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Organizational Affiliation: 

Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon genes protein	A	242	Homo sapiens	Mutation(s): 0  Gene Names: TMEM173, ERIS, MITA, STING, STING1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WV6 (Homo sapiens) Explore Q86WV6  Go to UniProtKB:  Q86WV6
PHAROS:  Q86WV6 GTEx:  ENSG00000184584

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4UR	B [auth A]	3'2'-cGAMP C20 H24 N10 O13 P2 FAFONCPHZLORMH-INFSMZHSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4UR	Binding MOAD:  5BQX	Kd: 1600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.187 
• R-Value Observed: 0.191 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.061	α = 90
b = 111.061	β = 90
c = 35.889	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-05-29 
• Released Date: 2015-06-24 
Deposition Author(s): Wu, J., Zhang, X., Chen, Z.J., Chen, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	RO1-GM-079554
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	RO1-AI-093967

Revision History  

• Version 1.0: 2015-06-24
  Type: Initial release
  
• Version 1.1: 2015-07-22
  Changes: Database references
• Version 1.2: 2015-08-05
  Changes: Database references
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence