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- PDB-9zfo: Cryo-EM Structure of Human STAT2-USP18-ISG15 Complex -

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Basic information

Entry
Database: PDB / ID: 9zfo
TitleCryo-EM Structure of Human STAT2-USP18-ISG15 Complex
Components
  • Signal transducer and activator of transcription 2
  • Ubiquitin-like protein ISG15
  • Ubl carboxyl-terminal hydrolase 18
KeywordsSIGNALING PROTEIN / Deubiquitinating Enzyme / ISGylation / Transcription Factor
Function / homology
Function and homology information


ISGF3 complex / response to stilbenoid / positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway ...ISGF3 complex / response to stilbenoid / positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway / Interleukin-20 family signaling / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / regulation of mitochondrial fission / RSV-host interactions / regulation of protein phosphorylation / ubiquitin-like protein ligase binding / Regulation of IFNA/IFNB signaling / positive regulation of interleukin-10 production / protein deubiquitination / positive regulation of bone mineralization / cell surface receptor signaling pathway via JAK-STAT / negative regulation of protein ubiquitination / antiviral innate immune response / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / integrin-mediated signaling pathway / Regulation of NF-kappa B signaling / response to bacterium / Negative regulators of DDX58/IFIH1 signaling / regulation of protein stability / Termination of translesion DNA synthesis / defense response / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / modification-dependent protein catabolic process / response to peptide hormone / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / integrin binding / RNA polymerase II transcription regulator complex / response to virus / positive regulation of type II interferon production / protein tag activity / Interferon alpha/beta signaling / regulation of cell population proliferation / regulation of inflammatory response / ISG15-specific peptidase activity / molecular adaptor activity / defense response to virus / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / defense response to bacterium / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Signal transducer and activation of transcription 2, C-terminal / STAT2, SH2 domain / Signal transducer and activator of transcription 2 C terminal / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : / STAT transcription factor, coiled-coil domain / STAT protein, DNA binding domain ...Signal transducer and activation of transcription 2, C-terminal / STAT2, SH2 domain / Signal transducer and activator of transcription 2 C terminal / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : / STAT transcription factor, coiled-coil domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / Signal transducer and activator of transcription, linker domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / : / : / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / p53-like transcription factor, DNA-binding / SH2 domain / Papain-like cysteine peptidase superfamily / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-like protein ISG15 / Signal transducer and activator of transcription 2 / Ubl carboxyl-terminal hydrolase 18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsHuynh, K.W. / Yamaguchi, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2026
Title: Insight into the scaffolding function of USP18 from a high resolution cryo-EM structure of STAT2-USP18-ISG15 ternary complex
Authors: Huynh, K.W. / Plumb, R. / Healy, D.R. / Jove, V. / Ralph, E.C. / Lee, C.W. / Wheeler, H. / Levine, K. / Huang, Z. / Fennell, K. / Corpina, R.A. / Craig, T. / Wes, P.D. / Loria, P.M. / ...Authors: Huynh, K.W. / Plumb, R. / Healy, D.R. / Jove, V. / Ralph, E.C. / Lee, C.W. / Wheeler, H. / Levine, K. / Huang, Z. / Fennell, K. / Corpina, R.A. / Craig, T. / Wes, P.D. / Loria, P.M. / Schenone, M. / Han, S. / Wang, F. / Wu, H. / Yamaguchi, M.
History
DepositionDec 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: Ubl carboxyl-terminal hydrolase 18
S: Signal transducer and activator of transcription 2
I: Ubiquitin-like protein ISG15


Theoretical massNumber of molelcules
Total (without water)140,3753
Polymers140,3753
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Ubl carboxyl-terminal hydrolase 18 / 43 kDa ISG15-specific protease / hUBP43 / ISG15-specific-processing protease / Ubl thioesterase 18


Mass: 40401.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP18, ISG43 / Cell (production host): Epithelial / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: Q9UMW8, ubiquitinyl hydrolase 1
#2: Protein Signal transducer and activator of transcription 2 / p113


Mass: 82825.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT2 / Cell (production host): Epithelial / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: P52630
#3: Protein Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein / hUCRP


Mass: 17147.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISG15, G1P2, UCRP / Cell (production host): Epithelial / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: P05161
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human STAT2-USP18-ISG15 Protein Complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.156 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pFastbac
Buffer solutionpH: 8 / Details: 25mM HEPES (pH 8.0), 200mM NaCl and 1.0mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPES1
2200 mMSodium ChlorideNaCl1
31.0 mMTCEP1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.8 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16605
Details: Selectris Energy Filter was also used during data collection.

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.6.0particle selectionBlob Picker
2Topaz0.2.4particle selection
3EPU3.6.0.6389image acquisition
5cryoSPARC4.6.0CTF correctionPatch CTF Estimation
10cryoSPARC4.6.0initial Euler assignmentAb-Initio Reconstruction
13cryoSPARC4.6.03D reconstruction
14PHENIXdev_5395model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143496 / Symmetry type: POINT
RefinementHighest resolution: 3.05 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056769
ELECTRON MICROSCOPYf_angle_d0.9549159
ELECTRON MICROSCOPYf_dihedral_angle_d5.486883
ELECTRON MICROSCOPYf_chiral_restr0.0521049
ELECTRON MICROSCOPYf_plane_restr0.0091154

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