8YDN | pdb_00008ydn

Crystal structure of a STING from C. gigas in complex with c-di-GMP

PDB DOI: https://doi.org/10.2210/pdb8YDN/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Magallana gigas
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-21 Released: 2025-09-03
Deposition Author(s): Zhang, Y., Yu, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.268 (Depositor), 0.268 (DCC)
R-Value Work:
0.233 (Depositor), 0.233 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of TM-STING C-terminal domain from the Pacific Oyster Crassostrea gigas

Zhang, Y., Yu, F.

To be published.

Macromolecule Content

Total Structure Weight: 40.74 kDa
Atom Count: 1,534
Modeled Residue Count: 189
Deposited Residue Count: 354
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon genes protein	A	354	Magallana gigas	Mutation(s): 0 Gene Names: CGI_10003079
UniProt
Find proteins for K1QMA0 (Magallana gigas) Explore K1QMA0 Go to UniProtKB: K1QMA0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K1QMA0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2E (Subject of Investigation/LOI) Query on C2E Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.268 (Depositor), 0.268 (DCC)
R-Value Work: 0.233 (Depositor), 0.233 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.4	α = 90
b = 104.4	β = 90
c = 96.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-09-03
Type: Initial release

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.