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

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Basic information

Entry
Database: PDB / ID: 11rm
TitleCryo-EM structure of human exportin-1 conjugated with FR-027*
ComponentsExportin-1
KeywordsPROTEIN TRANSPORT / nuclear transport / inhibitor
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsWing, C.E. / Fung, H.Y.J. / Chook, Y.M.
Funding support United States, 5items
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, C.E. / Niesman, A.B. / Fung, H.Y.J. / Vanstreels, E. / Jacquemyn, M. / Boel, E. / Vankerckhoven, A. / Berckmans, Y. / ...Authors: Van Hauwenhuyse, J. / Reniers, F. / Persoons, L. / Noppen, S. / Wing, C.E. / Niesman, A.B. / Fung, H.Y.J. / Vanstreels, E. / Jacquemyn, M. / Boel, E. / Vankerckhoven, A. / Berckmans, Y. / Kwanten, B. / Coosemans, A. / Van den Mooter, G. / Chook, Y.M. / Dehaen, W. / Daelemans, D.
History
DepositionMar 10, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 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
A: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7902
Polymers123,6621
Non-polymers1271
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 Exportin-1 / Exp1 / Chromosome region maintenance 1 protein homolog


Mass: 123662.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GS remaining after TEV cleavage, covalently bound to FR-027* at C528
Source: (gene. exp.) Homo sapiens (human) / Gene: XPO1, CRM1 / Plasmid: pGEX4TT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14980
#2: Chemical ChemComp-A1DBJ / 1-methyl-4-nitro-1H-imidazole


Mass: 127.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3O2
Has ligand of interestY
Has protein modificationY

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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: Full-length human XPO1 conjugated to FR-027* / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.124 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.4
Details: 20 mM HEPES pH 7.4, 150 mM NaCl, 2 mM Mg(OAc)2, 2 mM TCEP, 0.025% Tyloxapol
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
2150 mMSodium chlorideNaCl1
32 mMMagnesium acetateMg(CH3COO)21
42 mMTCEP1
50.025 %Tyloxapol1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 280 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 magnification: 165000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 25729
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
8ISOLDEmodel fitting
9Cootmodel fitting
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
15PHENIX1.19.1_4122model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1867386 / Details: blob picking followed by Topaz picking
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 630291 / Symmetry type: POINT
Atomic model buildingB value: 179.36 / Protocol: OTHER / Space: REAL
Details: Initial models were docked into maps using UCSF ChimeraX then manually built using Isolde and Coot and refined in PHENIX
Atomic model buildingPDB-ID: 9OG9

9og9


Pdb chain-ID: A / Accession code: 9OG9 / Details: starting model for XPO1 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.95 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027222
ELECTRON MICROSCOPYf_angle_d0.4419788
ELECTRON MICROSCOPYf_dihedral_angle_d3.394925
ELECTRON MICROSCOPYf_chiral_restr0.0341121
ELECTRON MICROSCOPYf_plane_restr0.0031253

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