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- EMDB-70463: Cryo-EM structure of human exportin-1 conjugated with KPT-127 and... -

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Entry
Database: EMDB / ID: EMD-70463
TitleCryo-EM structure of human exportin-1 conjugated with KPT-127 and bound to human ASB8-ELOB/C
Map dataFinal EM map
Sample
  • Complex: Ternary complex of full-length human XPO1 conjugated to KPT-127 and bound to ASB8-ELOB/C
    • Protein or peptide: Exportin-1
    • Protein or peptide: Ankyrin repeat and SOCS box protein 8
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
  • Ligand: propan-2-yl 3-[3-(3-chlorophenyl)-1H-1,2,4-triazol-1-yl]propanoate
Keywordsnuclear export / inhibitor / protein degradation / PROTEIN TRANSPORT
Function / homology
Function and homology information


cellular response to triglyceride / cellular response to salt / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / nuclear export signal receptor activity / Rev-mediated nuclear export of HIV RNA / target-directed miRNA degradation / elongin complex / NEP/NS2 Interacts with the Cellular Export Machinery ...cellular response to triglyceride / cellular response to salt / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / nuclear export signal receptor activity / Rev-mediated nuclear export of HIV RNA / target-directed miRNA degradation / elongin complex / NEP/NS2 Interacts with the Cellular Export Machinery / nucleocytoplasmic transport / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / Maturation of DENV proteins / Maturation of hRSV A proteins / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ribosomal large subunit export from nucleus / Tat-mediated elongation of the HIV-1 transcript / Cajal body / ribosomal subunit export from nucleus / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / mRNA export from nucleus / Cyclin A/B1/B2 associated events during G2/M transition / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / NPAS4 regulates expression of target genes / protein export from nucleus / ribosomal small subunit export from nucleus / RNA Polymerase II Pre-transcription Events / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Transcriptional and post-translational regulation of MITF-M expression and activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / transcription corepressor binding / Downregulation of TGF-beta receptor signaling / TP53 Regulates Transcription of DNA Repair Genes / Heme signaling / Deactivation of the beta-catenin transactivating complex / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / RHO GTPases Activate Formins / Inactivation of CSF3 (G-CSF) signaling / Vif-mediated degradation of APOBEC3G / MAPK6/MAPK4 signaling / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / small GTPase binding / kinetochore / Regulation of expression of SLITs and ROBOs / Separation of Sister Chromatids / nuclear envelope / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ribosome biogenesis / protein-containing complex assembly / DNA-binding transcription factor binding / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / intracellular signal transduction / response to xenobiotic stimulus / protein ubiquitination / ribonucleoprotein complex / protein domain specific binding / regulation of transcription by RNA polymerase II / ubiquitin protein ligase binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat and SOCS box protein 8, SOCS box domain / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat ...Ankyrin repeat and SOCS box protein 8, SOCS box domain / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Elongin-C / Elongin B / Ankyrin repeats (many copies) / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Exportin-1 / Elongin-C / Elongin-B / Ankyrin repeat and SOCS box protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsWing CE / Fung HYJ / Chook YM
Funding support United States, 7 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP220582 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP180410 United States
Cancer Prevention and Research Institute of Texas (CPRIT)150053 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP170170 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144137 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM131963 United States
Welch FoundationI-1532 United States
CitationJournal: Nat Chem Biol / Year: 2025
Title: SINE compounds activate exportin 1 degradation through an allosteric mechanism.
Authors: Casey E Wing / Ho Yee Joyce Fung / Bert Kwanten / Tolga Cagatay / Ashley B Niesman / Maarten Jacquemyn / Mehdi Gharghabi / Brecht Permentier / Binita Shakya / Rhituparna Nandi / Joseph M ...Authors: Casey E Wing / Ho Yee Joyce Fung / Bert Kwanten / Tolga Cagatay / Ashley B Niesman / Maarten Jacquemyn / Mehdi Gharghabi / Brecht Permentier / Binita Shakya / Rhituparna Nandi / Joseph M Ready / Trinayan Kashyap / Sharon Shacham / Yosef Landesman / Rosa Lapalombella / Dirk Daelemans / Yuh Min Chook /
Abstract: Overexpression of exportin 1 (XPO1/CRM1) in cancer cells mislocalizes numerous cancer-related nuclear export cargoes. Covalent selective inhibitors of nuclear export (SINEs), including the cancer ...Overexpression of exportin 1 (XPO1/CRM1) in cancer cells mislocalizes numerous cancer-related nuclear export cargoes. Covalent selective inhibitors of nuclear export (SINEs), including the cancer drug selinexor, restore proper nuclear localization by blocking XPO1-cargo interaction. These inhibitors also induce XPO1 degradation through the Cullin-RING E3 ligase (CRL) substrate receptor ASB8. Here we present cryo-electron microscopy structures revealing ASB8 binding to a cryptic XPO1 site that is exposed upon SINE conjugation. Unlike typical molecular glue degraders that directly bridge CRLs and substrates, SINEs bind XPO1 independently of ASB8, triggering an allosteric mechanism that enables high-affinity ASB8 recruitment, leading to XPO1 ubiquitination and degradation. ASB8-mediated degradation is also triggered by the endogenous itaconate derivative 4-octyl itaconate, suggesting that synthetic XPO1 inhibitors exploit a native cellular mechanism. This allosteric XPO1 degradation mechanism expands known modes of targeted protein degradation beyond molecular glue degraders and proteolysis-targeting chimeras of CRL4.
History
DepositionApr 30, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70463.png

Downloads & links

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Map

FileDownload / File: emd_70463.map.gz / Format: CCP4 / Size: 448.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 490 pix.
= 357.7 Å		0.73 Å/pix.
x 490 pix.
= 357.7 Å		0.73 Å/pix.
x 490 pix.
= 357.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0483
Minimum - Maximum-0.1314394 - 0.343554
Average (Standard dev.)-0.000085767206 (±0.005439318)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions490490490
Spacing490490490
CellA=B=C: 357.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_70463_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_70463_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of full-length human XPO1 conjugated to KPT-127 a...

EntireName: Ternary complex of full-length human XPO1 conjugated to KPT-127 and bound to ASB8-ELOB/C
Components
  • Complex: Ternary complex of full-length human XPO1 conjugated to KPT-127 and bound to ASB8-ELOB/C
    • Protein or peptide: Exportin-1
    • Protein or peptide: Ankyrin repeat and SOCS box protein 8
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
  • Ligand: propan-2-yl 3-[3-(3-chlorophenyl)-1H-1,2,4-triazol-1-yl]propanoate

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Supramolecule #1: Ternary complex of full-length human XPO1 conjugated to KPT-127 a...

SupramoleculeName: Ternary complex of full-length human XPO1 conjugated to KPT-127 and bound to ASB8-ELOB/C
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 178 KDa

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Macromolecule #1: Exportin-1

MacromoleculeName: Exportin-1 / type: protein_or_peptide / ID: 1 / Details: GS remaining after TEV cleavage / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 123.662484 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSMPAIMTML ADHAARQLLD FSQKLDINLL DNVVNCLYHG EGAQQRMAQE VLTHLKEHPD AWTRVDTILE FSQNMNTKYY GLQILENVI KTRWKILPRN QCEGIKKYVV GLIIKTSSDP TCVEKEKVYI GKLNMILVQI LKQEWPKHWP TFISDIVGAS R TSESLCQN ...String:
GSMPAIMTML ADHAARQLLD FSQKLDINLL DNVVNCLYHG EGAQQRMAQE VLTHLKEHPD AWTRVDTILE FSQNMNTKYY GLQILENVI KTRWKILPRN QCEGIKKYVV GLIIKTSSDP TCVEKEKVYI GKLNMILVQI LKQEWPKHWP TFISDIVGAS R TSESLCQN NMVILKLLSE EVFDFSSGQI TQVKSKHLKD SMCNEFSQIF QLCQFVMENS QNAPLVHATL ETLLRFLNWI PL GYIFETK LISTLIYKFL NVPMFRNVSL KCLTEIAGVS VSQYEEQFVT LFTLTMMQLK QMLPLNTNIR LAYSNGKDDE QNF IQNLSL FLCTFLKEHD QLIEKRLNLR ETLMEALHYM LLVSEVEETE IFKICLEYWN HLAAELYRES PFSTSASPLL SGSQ HFDVP PRRQLYLPML FKVRLLMVSR MAKPEEVLVV ENDQGEVVRE FMKDTDSINL YKNMRETLVY LTHLDYVDTE RIMTE KLHN QVNGTEWSWK NLNTLCWAIG SISGAMHEED EKRFLVTVIK DLLGLCEQKR GKDNKAIIAS NIMYIVGQYP RFLRAH WKF LKTVVNKLFE FMHETHDGVQ DMACDTFIKI AQKCRRHFVQ VQVGEVMPFI DEILNNINTI ICDLQPQQVH TFYEAVG YM IGAQTDQTVQ EHLIEKYMLL PNQVWDSIIQ QATKNVDILK DPETVKQLGS ILKTNVRACK AVGHPFVIQL GRIYLDML N VYKCLSENIS AAIQANGEMV TKQPLIRSMR TVKRETLKLI SGWVSRSNDP QMVAENFVPP LLDAVLIDYQ RNVPAAREP EVLSTMAIIV NKLGGHITAE IPQIFDAVFE CTLNMINKDF EEYPEHRTNF FLLLQAVNSH CFPAFLAIPP TQFKLVLDSI IWAFKHTMR NVADTGLQIL FTLLQNVAQE EAAAQSFYQT YFCDILQHIF SVVTDTSHTA GLTMHASILA YMFNLVEEGK I STSLNPGN PVNNQIFLQE YVANLLKSAF PHLQDAQVKL FVTGLFSLNQ DIPAFKEHLR DFLVQIKEFA GEDTSDLFLE ER EIALRQA DEEKHKRQMS VPGIFNPHEI PEEMCD

UniProtKB: Exportin-1

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Macromolecule #2: Ankyrin repeat and SOCS box protein 8

MacromoleculeName: Ankyrin repeat and SOCS box protein 8 / type: protein_or_peptide / ID: 2 / Details: GS remaining after TEV cleavage / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.869162 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSSLSERLIR TIAAIRSFPH DNVEDLIRGG ADVNCTHGTL KPLHCACMVS DADCVELLLE KGAEVNALDG YNRTALHYAA EKDEACVEV LLEYGANPNA LDGNRDTPLH WAAFKNNAEC VRALLESGAS VNALDYNNDT PLSWAAMKGN LESVSILLDY G AEVRVINL ...String:
GSSLSERLIR TIAAIRSFPH DNVEDLIRGG ADVNCTHGTL KPLHCACMVS DADCVELLLE KGAEVNALDG YNRTALHYAA EKDEACVEV LLEYGANPNA LDGNRDTPLH WAAFKNNAEC VRALLESGAS VNALDYNNDT PLSWAAMKGN LESVSILLDY G AEVRVINL IGQTPISRLV ALLVRGLGTE KEDSCFELLH RAVGHFELRK NGTMPREVAR DPQLCEKLTV LCSAPGTLKT LA RYAVRRS LGLQYLPDAV KGLPLPASLK EYLLLLE

UniProtKB: Ankyrin repeat and SOCS box protein 8

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Macromolecule #3: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.974616 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MMYVKLISSD GHEFIVKREH ALTSGTIKAM LSGPGQFAEN ETNEVNFREI PSHVLSKVCM YFTYKVRYTN SSTEIPEFPI APEIALELL MAANFLDC

UniProtKB: Elongin-C

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Macromolecule #4: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 4 / Details: full-length, wildtype / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.147781 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ

UniProtKB: Elongin-B

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Macromolecule #5: propan-2-yl 3-[3-(3-chlorophenyl)-1H-1,2,4-triazol-1-yl]propanoate

MacromoleculeName: propan-2-yl 3-[3-(3-chlorophenyl)-1H-1,2,4-triazol-1-yl]propanoate
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1CBC
Molecular weightTheoretical: 293.749 Da

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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

Concentration0.8 mg/mL
BufferpH: 7.4
Details: 20 mM HEPES pH 7.4, 110 mM KOAc, 2 mM Mg(OAc)2, 2 mM TCEP
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
SoftwareName: SerialEM
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 7946 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1092211 / Details: blob picking followed by Topaz picking
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: selinexor-XPO1-ASB8(R197A)-ELOB/C final map from this study
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 118442
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
chain_id: A, source_name: Other, initial_model_type: experimental modelstarting model for XPO1 from final model of selinexor-XPO1-ASB8(R197A)-ELOB/C in this study
chain_id: B, source_name: Other, initial_model_type: experimental modelstarting model for ASB8 from final model of selinexor-XPO1-ASB8(R197A)-ELOB/C in this study
chain_id: E, source_name: Other, initial_model_type: experimental modelstarting model for ELOC from final model of selinexor-XPO1-ASB8(R197A)-ELOB/C in this study
chain_id: F, source_name: Other, initial_model_type: experimental modelstarting model for ELOB from final model of selinexor-XPO1-ASB8(R197A)-ELOB/C in this study
SoftwareName: UCSF ChimeraX
DetailsInitial models were docked into maps using UCSF ChimeraX then manually built using Isolde and Coot and refined in PHENIX
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 102.26
Output model

PDB-9oge:
Cryo-EM structure of human exportin-1 conjugated with KPT-127 and bound to human ASB8-ELOB/C

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