9OGD: Human exportin-1 conjugated with selinexor and

Cryo-EM structure of human exportin-1 conjugated with selinexor and bound to human ASB8(R197A)-ELOB/C. Determined by electron microscopy at 2.49 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 2.49 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,978
Mol. weight: 178.01 kDa
Ligands: V6A
Released: 26 Nov 2025

Explore 9OGD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OGD contains 79 α-helices and 18 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 52 helices, 0 β-strands

Element	Residues	Length
α-helix	220-232	13
α-helix	238-242	5
α-helix	246-249	4
α-helix	250-254	5
α-helix	258-272	15
α-helix	280-297	18
α-helix	304-310	7
α-helix	313-338	26
α-helix	344-357	14
α-helix	363-383	21
α-helix	406-422	17
α-helix	424-427	4
α-helix	449-467	19
α-helix	469-484	16
α-helix	491-503	13
α-helix	510-530	21
α-helix	534-549	16
α-helix	552-557	6
α-helix	559-572	14
α-helix	580-594	15
α-helix	596-598	3
α-helix	602-603	2
α-helix	610-616	7
α-helix	618-621	4
α-helix	627-642	16
α-helix	647-657	11
α-helix	659-674	16
α-helix	676-680	5
α-helix	682-702	21
α-helix	704-706	3
α-helix	707-735	29
α-helix	737-741	5
α-helix	743-764	22
α-helix	769-771	3
α-helix	772-776	5
α-helix	777-790	14
α-helix	798-811	14
α-helix	812-815	4
α-helix	819-835	17
α-helix	842-858	17
α-helix	861-865	5
α-helix	868-882	15
α-helix	887-904	18
α-helix	908-932	25
α-helix	936-938	3
α-helix	939-954	16
α-helix	970-985	16
α-helix	991-1003	13
α-helix	1004-1006	3
α-helix	1008-1025	18
α-helix	1032-1034	3
α-helix	1035-1054	20

Chain B: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	56-63	8
α-helix	66-73	8
α-helix	89-96	8
α-helix	98-106	9
α-helix	121-128	8
α-helix	131-139	9
α-helix	154-160	7
α-helix	164-172	9
α-helix	187-196	10
α-helix	202-215	14
β-strand	222	1	1
β-strand	225	1	1
α-helix	228-231	4
α-helix	234-245	12
α-helix	250-261	12
α-helix	267-270	4
α-helix	271-273	3
α-helix	278-284	7

Chain E: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	2
β-strand	28-32	5	2
α-helix	33-36	4
α-helix	40-45	6
β-strand	59-61	3	2
α-helix	67-82	16
α-helix	89-94	6
α-helix	97-109	13

Chain F: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	2
β-strand	10	1	3
β-strand	12-19	8	2
β-strand	23	1	4
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-45	4	2
β-strand	50	1	2
β-strand	56	1	4
β-strand	68	1	5
β-strand	71	1	5
α-helix	72	1
β-strand	73-79	7	2
β-strand	80-81	2	6
β-strand	84-85	2	6
α-helix	86-88	3
β-strand	90	1	3
α-helix	91-100	10
α-helix	101-103	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exportin-1	A	protein	1073	Homo sapiens	O14980 (AlphaFold model)
Ankyrin repeat and SOCS box protein 8	B	protein	274	Homo sapiens	Q9H765 (AlphaFold model)
Elongin-C	E	protein	97	Homo sapiens	Q15369 (AlphaFold model)
Elongin-B	F	protein	118	Homo sapiens	Q15370 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9OGD_1 Exportin-1 (chains A)
GSMPAIMTMLADHAARQLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHPD
AWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPT
CVEKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEV
FDFSSGQITQVKSKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPL
GYIFETKLISTLIYKFLNVPMFRNVSLKCLTEIAGVSVSQYEEQFVTLFTLTMMQLKQML
PLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHDQLIEKRLNLRETLMEALHYMLLVS
EVEETEIFKICLEYWNHLAAELYRESPFSTSASPLLSGSQHFDVPPRRQLYLPMLFKVRL
LMVSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYVDTERIMTE
KLHNQVNGTEWSWKNLNTLCWAIGSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNKA
IIASNIMYIVGQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRH
FVQVQVGEVMPFIDEILNNINTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKYM
LLPNQVWDSIIQQATKNVDILKDPETVKQLGSILKTNVRACKAVGHPFVIQLGRIYLDML
NVYKCLSENISAAIQANGEMVTKQPLIRSMRTVKRETLKLISGWVSRSNDPQMVAENFVP
PLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMINKDF
EEYPEHRTNFFLLLQAVNSHCFPAFLAIPPTQFKLVLDSIIWAFKHTMRNVADTGLQILF
TLLQNVAQEEAAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKI
STSLNPGNPVNNQIFLQEYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDF
LVQIKEFAGEDTSDLFLEEREIALRQADEEKHKRQMSVPGIFNPHEIPEEMCD

Sequence of entity 2 (B), FASTA

>9OGD_2 Ankyrin repeat and SOCS box protein 8 (chains B)
GSSLSERLIRTIAAIRSFPHDNVEDLIRGGADVNCTHGTLKPLHCACMVSDADCVELLLE
KGAEVNALDGYNRTALHYAAEKDEACVEVLLEYGANPNALDGNRDTPLHWAAFKNNAECV
RALLESGASVNALDYNNDTPLSWAAMKGNLESVSILLDYGAEVRVINLIGQTPISRLVAL
LVAGLGTEKEDSCFELLHRAVGHFELRKNGTMPREVARDPQLCEKLTVLCSAPGTLKTLA
RYAVRRSLGLQYLPDAVKGLPLPASLKEYLLLLE

Sequence of entity 3 (E), FASTA

>9OGD_3 Elongin-C (chains E)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 4 (F), FASTA

>9OGD_4 Elongin-B (chains F)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Ligands and cofactors

ID	Name	Formula	Copies
V6A	selinexor, bound form	C17 H13 F6 N7 O	1

Primary citation

SINE compounds activate exportin 1 degradation through an allosteric mechanism. Wing, C.E., Fung, H.Y.J., Kwanten, B. et al. Nat Chem Biol (2025) 21:2002-2013. DOI 10.1038/s41589-025-02058-0 · PubMed

Other PDB entries of the same protein (UniProt O14980 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1W9C 2.3 Å, Proteolytic fragment of CRM1 spanning six C-terminal HEAT repeats
7B51 2.58 Å, Crystal structure of human CRM1 covalently modified by 2-mercaptoethanol at Cys528
9HFL 2.62 Å, Cryo-EM structure of the human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and…
5DIS 2.85 Å, Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino acid…
3GB8 2.9 Å, Crystal structure of CRM1/Snurportin-1 complex
9B62 2.9 Å, Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model
9OG9 2.93 Å, Cryo-EM structure of human full-length XPO1 (unliganded)
11RM 2.95 Å, Cryo-EM structure of human exportin-1 conjugated with FR-027*
6TVO 3.2 Å, Human CRM1-RanGTP in complex with Leptomycin B
9OGB 3.25 Å, Cryo-EM structure of human exportin-1 conjugated with selinexor and bound to yeast…
9OGE 3.28 Å, Cryo-EM structure of human exportin-1 conjugated with KPT-127 and bound to human…
9OGA 3.37 Å, Cryo-EM structure of human full-length XPO1 conjugated with selinexor

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