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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Ligand Structure Quality Assessment

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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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

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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.