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- PDB-6nt5: Cryo-EM structure of full-length human STING in the apo state -

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Basic information

Entry
Database: PDB / ID: 6nt5
TitleCryo-EM structure of full-length human STING in the apo state
ComponentsStimulator of interferon protein
KeywordsIMMUNE SYSTEM / ER / membrane / adaptor
Function / homologyStimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / cyclic-di-GMP binding / activation of innate immune response / positive regulation of type I interferon production / Stimulator of interferon protein
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.1 Å resolution
AuthorsShang, G. / Zhang, C. / Chen, Z.J. / Bai, X. / Zhang, X.
Funding supportUnited States , 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM088197United States
National Institutes of Health/National Institute of General Medical SciencesR35GM130289United States
Howard Hughes Medical InstituteUnited States
Welch FoundationI-1389United States
Welch FoundationI-1702United States
Welch FoundationI-1944United States
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structures of STING reveal its mechanism of activation by cyclic GMP-AMP.
Authors: Guijun Shang / Conggang Zhang / Zhijian J Chen / Xiao-Chen Bai / Xuewu Zhang
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 28, 2019 / Release: Mar 6, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 6, 2019Structure modelrepositoryInitial release
1.1Mar 20, 2019Structure modelData collection / Database referencescitation / citation_author_citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: Stimulator of interferon protein
B: Stimulator of interferon protein


Theoretical massNumber of molelcules
Total (without water)85,9712
Polyers85,9712
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide Stimulator of interferon protein


Mass: 42985.379 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: STING, LOC340061, hCG_1782396 / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: A0A2R3XZB7

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: full-length human STING / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Cell: HEK293 GnTI- / Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 30

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 75479 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL

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