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- PDB-9oga: Cryo-EM structure of human full-length XPO1 conjugated with selinexor -

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Basic information

Entry
Database: PDB / ID: 9oga
TitleCryo-EM structure of human full-length XPO1 conjugated with selinexor
ComponentsExportin-1
KeywordsPROTEIN TRANSPORT / nuclear export / HEAT repeat / 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 / regulation of centrosome duplication / regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / 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 / regulation of centrosome duplication / regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / NEP/NS2 Interacts with the Cellular Export Machinery / nucleocytoplasmic transport / Maturation of hRSV A proteins / ribosomal large subunit export from nucleus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / protein localization to nucleus / mRNA export from nucleus / Cajal body / ribosomal subunit export from nucleus / Cyclin A/B1/B2 associated events during G2/M transition / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / NPAS4 regulates expression of target genes / Mitotic Prometaphase / Transcriptional and post-translational regulation of MITF-M expression and activity / EML4 and NUDC in mitotic spindle formation / protein export from nucleus / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / Deactivation of the beta-catenin transactivating complex / Heme signaling / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / kinetochore / small GTPase binding / Separation of Sister Chromatids / nuclear envelope / ribosome biogenesis / nuclear membrane / DNA-binding transcription factor binding / response to xenobiotic stimulus / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / nucleus / membrane / 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
selinexor, bound form / Exportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsWing, C.E. / Fung, H.Y.J. / Chook, Y.M.
Funding support United States, 7items
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)RP150053 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: To Be Published
Title: SINE compounds activate exportin-1 degradation via an allosteric mechanism
Authors: Wing, C.E. / Fung, H.Y.J. / Chook, Y.M.
History
DepositionApr 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data 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)124,1082
Polymers123,6621
Non-polymers4451
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 selinexor 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-V6A / selinexor, bound form / 3-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}-N'-(pyrazin-2-yl)propanehydrazide


Mass: 445.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13F6N7O / Feature type: SUBJECT OF INVESTIGATION
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: Human wildtype full-length exportin-1 (XPO1) covalently bound to selinexor
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) / Plasmid: pGEX4TT3
Buffer solutionpH: 7.4
Details: 20 mM HEPES pH 7.4, 110 mM KOAc, 2 mM Mg(OAc)2, 2 mM TCEP
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: 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 magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5852
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2Topazparticle selection
3SerialEMimage acquisition
5cryoSPARCCTF correction
8UCSF ChimeraXmodel fitting
9ISOLDEmodel fitting
10Cootmodel fitting
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
14cryoSPARCclassification
15cryoSPARC3D reconstruction
16PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1197263
Details: template picking using unliganded XPO1 from this study followed by Topaz picking
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 431664 / Symmetry type: POINT
Atomic model buildingB value: 148.94 / Protocol: OTHER / Space: REAL
Details: Initial model was docked into maps using UCSF ChimeraX then manually built using Isolde and Coot and refined in PHENIX
Atomic model buildingDetails: unliganded XPO1 from this study / Source name: Other / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 148.86 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00377575
ELECTRON MICROSCOPYf_angle_d0.58810265
ELECTRON MICROSCOPYf_chiral_restr0.03731172
ELECTRON MICROSCOPYf_plane_restr0.01491309
ELECTRON MICROSCOPYf_dihedral_angle_d7.9622982

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