4F5D | pdb_00004f5d

ERIS/STING in complex with ligand

• PDB DOI: https://doi.org/10.2210/pdb4F5D/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-05-13 Released: 2012-06-27 
• Deposition Author(s): Huang, Y.H., Liu, X.Y., Su, X.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.242 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

The structural basis for the sensing and binding of cyclic di-GMP by STING

Huang, Y.H., Liu, X.Y., Du, X.X., Jiang, Z.F., Su, X.D.

(2012) Nat Struct Mol Biol 19: 728-730

• PubMed: 22728659 
• DOI: https://doi.org/10.1038/nsmb.2333
• Primary Citation Related Structures: 
  4F5D, 4F5E


• PubMed Abstract: 
  

  STING (stimulator of interferon genes) is an essential signaling adaptor that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). STING's structure and its binding mechanism to cyclic dinucleotides were unknown. We report here the crystal structures of the STING cytoplasmic domain and its complex with c-di-GMP, thus providing the structural basis for understanding STING function.

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Organizational Affiliation: 
• State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 57.99 kDa 
• Atom Count: 3,092 
• Modeled Residue Count: 376 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein 173	A, B	256	Homo sapiens	Mutation(s): 1  Gene Names: TMEM173, ERIS, MITA, STING
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	C [auth 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) C20 H24 N10 O14 P2 PKFDLKSEZWEFGL-MHARETSRSA-N
MG	D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.242 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.85	α = 90
b = 111.85	β = 90
c = 35.02	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Huang, Y.H., Liu, X.Y., Su, X.D.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary