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- EMDB-70461: Cryo-EM structure of human exportin-1 conjugated with KPT-185 and... -

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Entry
Database: EMDB / ID: EMD-70461
TitleCryo-EM structure of human exportin-1 conjugated with KPT-185 and bound to human ASB8-ELOB/C
Map dataFinal volume from cryoSPARC z-flipped using ChimeraX
Sample
  • Complex: Ternary complex of full-length human XPO1 conjugated to KPT-185 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-methoxy-5-(trifluoromethyl)phenyl]-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 / regulation of centrosome duplication / regulation of protein export from nucleus / target-directed miRNA degradation / elongin complex ...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 / target-directed miRNA degradation / elongin complex / Rev-mediated nuclear export of HIV RNA / NEP/NS2 Interacts with the Cellular Export Machinery / VCB complex / nucleocytoplasmic transport / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / 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 / ribosomal large subunit export from nucleus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / protein localization to nucleus / Tat-mediated elongation of the HIV-1 transcript / mRNA export from nucleus / Formation of HIV-1 elongation complex containing HIV-1 Tat / Cajal body / Formation of HIV elongation complex in the absence of HIV Tat / ribosomal subunit 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 / ribosomal small subunit export from nucleus / NPAS4 regulates expression of target genes / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RNA Polymerase II Pre-transcription Events / Transcriptional and post-translational regulation of MITF-M expression and activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein export from nucleus / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / Deactivation of the beta-catenin transactivating complex / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Heme signaling / RHO GTPases Activate Formins / Vif-mediated degradation of APOBEC3G / MAPK6/MAPK4 signaling / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / kinetochore / Evasion by RSV of host interferon responses / small GTPase binding / Regulation of expression of SLITs and ROBOs / Separation of Sister Chromatids / nuclear envelope / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ribosome biogenesis / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / nuclear membrane / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / intracellular signal transduction / protein ubiquitination / response to xenobiotic stimulus / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / nucleus / membrane / 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 / Ankyrin repeats (many copies) / Elongin-C / Elongin B / 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 repeats (3 copies) / Ankyrin repeat profile. / 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: 3.37 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: bioRxiv / Year: 2025
Title: SINE compounds activate exportin-1 degradation via an allosteric mechanism.
Authors: Casey Elizabeth Wing / Ho Yee Joyce Fung / Bert Kwanten / Tolga Cagatay / Ashley B Niesman / Maarten Jacquemyn / Mehdi Gharghabi / Brecht Permentier / Binita Shakya / Rhituparna Nandi / ...Authors: Casey Elizabeth 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: The nuclear export receptor exportin 1 (XPO1/CRM1) is often overexpressed in cancer cells, leading to the mislocalization of numerous cancer-related protein cargoes . Selinexor, a covalent XPO1 ...The nuclear export receptor exportin 1 (XPO1/CRM1) is often overexpressed in cancer cells, leading to the mislocalization of numerous cancer-related protein cargoes . Selinexor, a covalent XPO1 inhibitor, and other Selective Inhibitor of Nuclear Export (SINEs) restore proper nuclear localization by blocking XPO1-cargo binding . SINEs also induce XPO1 degradation via the Cullin-RING E3 ubiquitin ligase (CRL) substrate receptor ASB8 . Here we elucidate the mechanism underlying the high-affinity engagement of CRL5 with SINE-conjugated XPO1. Cryogenic electron microscopy (cryoEM) structures reveal that ASB8 binds to a cryptic site on XPO1, which becomes accessible only upon SINE conjugation. While molecular glue degraders typically interact with both CRL and the substrate , SINEs bind to XPO1 without requiring interaction with ASB8 for efficient XPO1 degradation. Instead, an allosteric mechanism facilitates high affinity XPO1-ASB8 interaction, leading to XPO1 ubiquitination and degradation. ASB8-mediated degradation is also observed upon treatment of the endogenous itaconate derivate 4-octyl itaconate, which suggests a native mechanism that is inadvertently exploited by synthesized XPO1 inhibitors. This allosteric XPO1 degradation mechanism of SINE compounds expands the known modes of targeted protein degradation beyond the well-characterized molecular glue degraders and proteolysis targeting chimeras of CRL4.
History
DepositionApr 30, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70461.png

Downloads & links

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Map

FileDownload / File: emd_70461.map.gz / Format: CCP4 / Size: 172.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal volume from cryoSPARC z-flipped using ChimeraX
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 356 pix.
= 299.04 Å		0.84 Å/pix.
x 356 pix.
= 299.04 Å		0.84 Å/pix.
x 356 pix.
= 299.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0586
Minimum - Maximum-0.13367067 - 0.40435222
Average (Standard dev.)0.0013610631 (±0.009993752)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions356356356
Spacing356356356
CellA=B=C: 299.03998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhancer map used to help modeling of XPO1 N and C-terminus

Fileemd_70461_additional_1.map
AnnotationDeepEMhancer map used to help modeling of XPO1 N and C-terminus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A from cryoSPARC z-flipped using ChimeraX

Fileemd_70461_half_map_1.map
AnnotationHalf-map A from cryoSPARC z-flipped using ChimeraX
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B from cryoSPARC z-flipped using ChimeraX

Fileemd_70461_half_map_2.map
AnnotationHalf-map B from cryoSPARC z-flipped using ChimeraX
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-185 a...

EntireName: Ternary complex of full-length human XPO1 conjugated to KPT-185 and bound to ASB8-ELOB/C
Components
  • Complex: Ternary complex of full-length human XPO1 conjugated to KPT-185 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-methoxy-5-(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}propanoate

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Supramolecule #1: Ternary complex of full-length human XPO1 conjugated to KPT-185 a...

SupramoleculeName: Ternary complex of full-length human XPO1 conjugated to KPT-185 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-methoxy-5-(trifluoromethyl)phenyl]-1H-1,2,4-t...

MacromoleculeName: propan-2-yl 3-{3-[3-methoxy-5-(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}propanoate
type: ligand / ID: 5 / Number of copies: 1 / Formula: K85
Molecular weightTheoretical: 357.328 Da
Chemical component information

ChemComp-K85:
propan-2-yl 3-{3-[3-methoxy-5-(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}propanoate

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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

Concentration0.4 mg/mL
BufferpH: 7.4
Details: 20 mM HEPES pH 7.4, 110 mM KOAc, 2 mM Mg(OAc)2, 2 mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / 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: GIF Bioquantum / Energy filter - Slit width: 10 eV
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4746 / 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: 1.1 µm / Nominal magnification: 105000
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: 1066266 / Details: blob picking followed by Topaz picking
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 205462
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
ChainDetailsPDB ID
chain_id: B, source_name: Other, initial_model_type: experimental modelstarting model for XPO1 from final model of selinexor-XPO1 in this study
chain_id: D, source_name: PDB, initial_model_type: experimental modelstarting model for ELOC

6v9h

chain_id: E, source_name: PDB, initial_model_type: experimental modelstarting model for ELOB

6v9h

chain_id: A, source_name: AlphaFold, initial_model_type: in silico modelstarting model for ASB8

5-f1

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: 183.84
Output model

PDB-9ogc:
Cryo-EM structure of human exportin-1 conjugated with KPT-185 and bound to human ASB8-ELOB/C

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