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- EMDB-71619: STING oligomer bound to PI(3,5)P2 without C53 or STG2 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-71619
TitleSTING oligomer bound to PI(3,5)P2 without C53 or STG2
Map data
Sample
  • Complex: STING oligomer bound to its ligand cGAMP, Cholesteryl hemisuccinate and PI(3,5)P2
KeywordsSTING / lipid / oligomerization / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLi J / Zhang X / Bai X
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA273595 United States
Welch FoundationI-1702 United States
Welch FoundationI-1944 United States
CitationJournal: To Be Published
Title: Structural basis for the roles of phosphoinositide phosphates and cholesterol in STING activation
Authors: Jie L / Zhang X / Bai X
History
DepositionJul 7, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71619.png

Downloads & links

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Map

FileDownload / File: emd_71619.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 240 pix.
= 198.24 Å		0.83 Å/pix.
x 240 pix.
= 198.24 Å		0.83 Å/pix.
x 240 pix.
= 198.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0017
Minimum - Maximum-0.007047229 - 0.0122719025
Average (Standard dev.)0.00003777206 (±0.0004393147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 198.23999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71619_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71619_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : STING oligomer bound to its ligand cGAMP, Cholesteryl hemisuccina...

EntireName: STING oligomer bound to its ligand cGAMP, Cholesteryl hemisuccinate and PI(3,5)P2
Components
  • Complex: STING oligomer bound to its ligand cGAMP, Cholesteryl hemisuccinate and PI(3,5)P2

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Supramolecule #1: STING oligomer bound to its ligand cGAMP, Cholesteryl hemisuccina...

SupramoleculeName: STING oligomer bound to its ligand cGAMP, Cholesteryl hemisuccinate and PI(3,5)P2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

29282

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 39819
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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