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- EMDB-74146: Cryo-EM Structure of Human STAT2-USP18-ISG15 Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-74146
TitleCryo-EM Structure of Human STAT2-USP18-ISG15 Complex
Map dataHuman STAT2-USP18-ISG15 Complex
Sample
  • Complex: Human STAT2-USP18-ISG15 Protein Complex
    • Protein or peptide: Ubl carboxyl-terminal hydrolase 18
    • Protein or peptide: Signal transducer and activator of transcription 2
    • Protein or peptide: Ubiquitin-like protein ISG15
KeywordsDeubiquitinating Enzyme / ISGylation / Transcription Factor / SIGNALING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsHuynh KW / Yamaguchi M
Funding support1 items
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 KW / Plumb R / Healy DR / Jove V / Ralph EC / Lee CW / Wheeler H / Levine K / Huang Z / Fennell K / Corpina RA / Craig T / Wes PD / Loria PM / Schenone M / Han S / Wang F / Wu H / Yamaguchi M
History
DepositionDec 1, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74146.png

Downloads & links

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Map

FileDownload / File: emd_74146.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman STAT2-USP18-ISG15 Complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 360 pix.
= 270. Å		0.75 Å/pix.
x 360 pix.
= 270. Å		0.75 Å/pix.
x 360 pix.
= 270. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.046
Minimum - Maximum-0.47803247 - 0.6553332
Average (Standard dev.)-0.000002270724 (±0.009976419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human STAT2-USP18-ISG15 Complex

Fileemd_74146_half_map_1.map
AnnotationHuman STAT2-USP18-ISG15 Complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human STAT2-USP18-ISG15 Complex

Fileemd_74146_half_map_2.map
AnnotationHuman STAT2-USP18-ISG15 Complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human STAT2-USP18-ISG15 Protein Complex

EntireName: Human STAT2-USP18-ISG15 Protein Complex
Components
  • Complex: Human STAT2-USP18-ISG15 Protein Complex
    • Protein or peptide: Ubl carboxyl-terminal hydrolase 18
    • Protein or peptide: Signal transducer and activator of transcription 2
    • Protein or peptide: Ubiquitin-like protein ISG15

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Supramolecule #1: Human STAT2-USP18-ISG15 Protein Complex

SupramoleculeName: Human STAT2-USP18-ISG15 Protein Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 156 KDa

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Macromolecule #1: Ubl carboxyl-terminal hydrolase 18

MacromoleculeName: Ubl carboxyl-terminal hydrolase 18 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.401734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LEEKKEEDSN MKREQPRERP RAWDYPHGLV GLHNIGQTCC LNSLIQVFVM NVDFTRILKR ITVPRGADEQ RRSVPFQMLL LLEKMQDSR QKAVRPLELA YCLQKCNVPL FVQHDAAQLY LKLWNLIKDQ ITDVHLVERL QALYTIRVKD SLICVDCAME S SRNSSMLT ...String:
LEEKKEEDSN MKREQPRERP RAWDYPHGLV GLHNIGQTCC LNSLIQVFVM NVDFTRILKR ITVPRGADEQ RRSVPFQMLL LLEKMQDSR QKAVRPLELA YCLQKCNVPL FVQHDAAQLY LKLWNLIKDQ ITDVHLVERL QALYTIRVKD SLICVDCAME S SRNSSMLT LPLSLFDVDS KPLKTLEDAL HCFFQPRELS SKSKCFCENC GKKTRGKQVL KLTHLPQTLT IHLMRFSIRN SQ TRKICHS LYFPQSLDFS QILPMKRESC DAEEQSGGQY ELFAVIAHVG MADSGHYCVY IRNAVDGKWF CFNDSNICLV SWE DIQCTY GNPNYHWQET AYLLVYMKME C

UniProtKB: Ubl carboxyl-terminal hydrolase 18

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Macromolecule #2: Signal transducer and activator of transcription 2

MacromoleculeName: Signal transducer and activator of transcription 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.825812 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAQWEMLQNL DSPFQDQLHQ LYSHSLLPVD IRQYLAVWIE DQNWQEAALG SDDSKATMLF FHFLDQLNYE CGRCSQDPES LLLQHNLRK FCRDIQPFSQ DPTQLAEMIF NLLLEEKRIL IQAQRAQLEQ GEPVLETPVE SQQHEIESRI LDLRAMMEKL V KSISQLKD ...String:
MAQWEMLQNL DSPFQDQLHQ LYSHSLLPVD IRQYLAVWIE DQNWQEAALG SDDSKATMLF FHFLDQLNYE CGRCSQDPES LLLQHNLRK FCRDIQPFSQ DPTQLAEMIF NLLLEEKRIL IQAQRAQLEQ GEPVLETPVE SQQHEIESRI LDLRAMMEKL V KSISQLKD QQDVFCFRYK IQAKGKTPSL DPHQTKEQKI LQETLNELDK RRKEVLDASK ALLGRLTTLI ELLLPKLEEW KA QQQKACI RAPIDHGLEQ LETWFTAGAK LLFHLRQLLK ELKGLSCLVS YQDDPLTKGV DLRNAQVTEL LQRLLHRAFV VET QPCMPQ TPHRPLILKT GSKFTVRTRL LVRLQEGNES LTVEVSIDRN PPQLQGFRKF NILTSNQKTL TPEKGQSQGL IWDF GYLTL VEQRSGGSGK GSNKGPLGVT EELHIISFTV KYTYQGLKQE LKTDTLPVVI ISNMNQLSIA WASVLWFNLL SPNLQ NQQF FSNPPKAPWS LLGPALSWQF SSYVGRGLNS DQLSMLRNKL FGQNCRTEDP LLSWADFTKR ESPPGKLPFW TWLDKI LEL VHDHLKDLWN DGRIMGFVSR SQERRLLKKT MSGTFLLRFS ESSEGGITCS WVEHQDDDKV LIYSVQPYTK EVLQSLP LT EIIRHYQLLT EENIPENPLR FLYPRIPRDE AFGCYYQEKV NLQERRKYLK HRLIVVSNRQ VDELQQPLEL K

UniProtKB: Signal transducer and activator of transcription 2

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Macromolecule #3: Ubiquitin-like protein ISG15

MacromoleculeName: Ubiquitin-like protein ISG15 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.147637 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MGWDLTVKML AGNEFQVSLS SSMSVSELKA QITQKIGVHA FQQRLAVHPS GVALQDRVPL ASQGLGPGST VLLVVDKSDE PLSILVRNN KGRSSTYEVR LTQTVAHLKQ QVSGLEGVQD DLFWLTFEGK PLEDQLPLGE YGLKPLSTVF MNLRLRGG

UniProtKB: Ubiquitin-like protein ISG15

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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

Concentration0.80 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMHEPES
200.0 mMSodium ChlorideNaCl
1.0 mMTCEP

Details: 25mM HEPES (pH 8.0), 200mM NaCl and 1.0mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 16605 / Average exposure time: 2.8 sec. / Average electron dose: 40.0 e/Å2
Details: Selectris Energy Filter was also used during data collection.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Software - details: Patch CTF Estimation / Type: NONE
Startup modelType of model: OTHER
Details: Initial model was generated in CryoSPARC using the Ab Initio Reconstruction method.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 143496
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0) / Software - details: Ab-Initio Reconstruction / Details: All refinement steps are done in CryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: All refinement steps are done in CryoSPARC
FSC plot (resolution estimation)

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