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- EMDB-75979: Cryo-EM structure of human exportin-1 conjugated with FR-027* -

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Basic information

Entry
Database: EMDB / ID: EMD-75979
TitleCryo-EM structure of human exportin-1 conjugated with FR-027*
Map data
Sample
  • Complex: Full-length human XPO1 conjugated to FR-027*
    • Protein or peptide: Exportin-1
  • Ligand: 1-methyl-4-nitro-1H-imidazole
Keywordsnuclear transport / inhibitor / 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 / NEP/NS2 Interacts with the Cellular Export Machinery / nucleocytoplasmic transport / Maturation of hRSV A proteins ...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 / NEP/NS2 Interacts with the Cellular Export Machinery / nucleocytoplasmic transport / Maturation of hRSV A proteins / Maturation of DENV proteins / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ribosomal large subunit export from nucleus / Cajal body / ribosomal subunit export from nucleus / mRNA export from nucleus / Cyclin A/B1/B2 associated events during G2/M transition / NPAS4 regulates expression of target genes / protein export from nucleus / ribosomal small subunit export from nucleus / 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 / Downregulation of TGF-beta receptor signaling / Heme signaling / Deactivation of the beta-catenin transactivating complex / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / small GTPase binding / kinetochore / Separation of Sister Chromatids / nuclear envelope / ribosome biogenesis / DNA-binding transcription factor binding / response to xenobiotic stimulus / ribonucleoprotein complex / protein domain specific binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
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, 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsWing CE / Fung HYJ / Chook YM
Funding support United States, 5 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP220582 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM154185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144137 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP210041 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM131963 United States
CitationJournal: Nat Commun / Year: 2026
Title: Preclinical characterization of a reversible XPO1 inhibitor for cancer therapy
Authors: Van Hauwenhuyse J / Reniers F / Persoons L / Noppen S / Wing CE / Niesman AB / Fung HYJ / Vanstreels E / Jacquemyn M / Boel E / Vankerckhoven A / Berckmans Y / Kwanten B / Coosemans A / Van ...Authors: Van Hauwenhuyse J / Reniers F / Persoons L / Noppen S / Wing CE / Niesman AB / Fung HYJ / Vanstreels E / Jacquemyn M / Boel E / Vankerckhoven A / Berckmans Y / Kwanten B / Coosemans A / Van den Mooter G / Chook YM / Dehaen W / Daelemans D
History
DepositionMar 10, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75979.png

Downloads & links

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Map

FileDownload / File: emd_75979.map.gz / Format: CCP4 / Size: 142.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 334 pix.
= 243.686 Å		0.73 Å/pix.
x 334 pix.
= 243.686 Å		0.73 Å/pix.
x 334 pix.
= 243.686 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0463
Minimum - Maximum-0.1191511 - 0.29008734
Average (Standard dev.)0.00017158088 (±0.00784622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions334334334
Spacing334334334
CellA=B=C: 243.6864 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75979_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75979_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 : Full-length human XPO1 conjugated to FR-027*

EntireName: Full-length human XPO1 conjugated to FR-027*
Components
  • Complex: Full-length human XPO1 conjugated to FR-027*
    • Protein or peptide: Exportin-1
  • Ligand: 1-methyl-4-nitro-1H-imidazole

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Supramolecule #1: Full-length human XPO1 conjugated to FR-027*

SupramoleculeName: Full-length human XPO1 conjugated to FR-027* / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 124 KDa

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Macromolecule #1: Exportin-1

MacromoleculeName: Exportin-1 / type: protein_or_peptide / ID: 1
Details: GS remaining after TEV cleavage, covalently bound to FR-027* at C528
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: 1-methyl-4-nitro-1H-imidazole

MacromoleculeName: 1-methyl-4-nitro-1H-imidazole / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1DBJ
Molecular weightTheoretical: 127.101 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

Concentration3 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMSodium chlorideNaCl
2.0 mMMagnesium acetateMg(CH3COO)2
2.0 mMTCEP
0.025 %Tyloxapol

Details: 20 mM HEPES pH 7.4, 150 mM NaCl, 2 mM Mg(OAc)2, 2 mM TCEP, 0.025% Tyloxapol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 280 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: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 25729 / 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 / Cs: 2.7 mm / 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: 1867386 / Details: blob picking followed by Topaz picking
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9og9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 630291
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 modelPDB ID:

9og9


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: starting model for XPO1
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: 179.36
Output model

PDB-11rm:
Cryo-EM structure of human exportin-1 conjugated with FR-027*

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