9HFL: Exportin-1

Cryo-EM structure of the human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and capped-RNA. Determined by electron microscopy at 2.62 Å resolution. Released 16 Jul 2025.

Method: Electron microscopy
Resolution: 2.62 Å
Organism: Homo sapiens
Chains: 7
Atoms: 17,802
Mol. weight: 352.66 kDa
Ligands: GTA, MG, GTP
Released: 16 Jul 2025

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

Secondary structure: helices and β-sheets

9HFL contains 138 α-helices and 24 β-strands across 5 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: 68 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
α-helix	25-37	13
α-helix	41-55	15
α-helix	60-69	10
α-helix	73-90	18
α-helix	96-115	20
α-helix	117-122	6
α-helix	125-141	17
α-helix	149-159	11
α-helix	161-175	15
α-helix	176-180	5
α-helix	188-200	13
α-helix	202-215	14
α-helix	219-232	14
α-helix	239-242	4
α-helix	246-249	4
α-helix	250-254	5
α-helix	261-273	13
α-helix	280-297	18
α-helix	304-310	7
α-helix	313-338	26
α-helix	341-343	3
α-helix	344-358	15
α-helix	363-383	21
α-helix	401-403	3
α-helix	404-422	19
α-helix	424-426	3
β-strand	430-434	5	1
β-strand	440-444	5	1
α-helix	449-467	19
α-helix	469-485	17
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	743-765	23
α-helix	769-775	7
α-helix	777-780	4
α-helix	781-785	5
α-helix	786-790	5
α-helix	793-795	3
α-helix	798-811	14
α-helix	812-814	3
α-helix	816-818	3
α-helix	819-831	13
α-helix	842-858	17
α-helix	860-864	5
α-helix	868-882	15
α-helix	887-906	20
α-helix	908-930	23
α-helix	933-938	6
α-helix	939-955	17
α-helix	970-985	16
α-helix	991-1003	13
α-helix	1008-1021	14
α-helix	1035-1054	20

Chain B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	2
α-helix	23-32	10
α-helix	34-36	3
β-strand	45-54	10	2
β-strand	57-66	10	2
α-helix	76-79	4
β-strand	85-91	7	2
α-helix	95-99	5
α-helix	101-111	11
β-strand	117-122	6	2
α-helix	133-135	3
α-helix	138-142	5
α-helix	144	1
β-strand	145-148	4	2
β-strand	150	1	3
β-strand	155	1	3
α-helix	159-169	11
β-strand	176	1	2

Chain C: 50 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	26-37	12
α-helix	46-60	15
α-helix	65-78	14
α-helix	80-82	3
α-helix	83-96	14
α-helix	98-117	20
α-helix	121-136	16
β-strand	140	1	4
α-helix	142-154	13
α-helix	155-157	3
α-helix	163-175	13
α-helix	177-187	11
α-helix	189-204	16
α-helix	211-214	4
β-strand	217	1	5
β-strand	227	1	6
α-helix	228-241	14
α-helix	252-256	5
α-helix	257-261	5
α-helix	264-265	2
β-strand	266	1	4
α-helix	268-271	4
α-helix	273-275	3
α-helix	283-285	3
β-strand	287	1	6
α-helix	294-296	3
α-helix	302-305	4
α-helix	309-324	16
α-helix	329-337	9
α-helix	347-359	13
α-helix	369-382	14
α-helix	387-400	14
β-strand	405	1	5
α-helix	407-422	16
α-helix	430-438	9
α-helix	444-458	15
α-helix	462-468	7
α-helix	471-476	6
α-helix	478-480	3
α-helix	491-494	4
α-helix	498-509	12
α-helix	514-521	8
α-helix	525-526	2
α-helix	541-554	14
α-helix	559-568	10
α-helix	570-576	7
α-helix	580-593	14
α-helix	598-610	13
α-helix	616-623	8
α-helix	635-673	39
α-helix	686-731	46
α-helix	738-753	16
α-helix	755-759	5
α-helix	762-764	3
α-helix	765-769	5
α-helix	776-787	12

Chain D: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	13-15	3
α-helix	29-37	9
β-strand	41-45	5	7
α-helix	53-60	8
β-strand	66-73	8	7
β-strand	80-88	9	7
α-helix	91-96	6
α-helix	97-101	5
β-strand	105-106	2	8
β-strand	109-110	2	8
β-strand	112-116	5	7
β-strand	125	1	7
α-helix	134-138	5
α-helix	144-146	3

Chain P: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	117-135	19
α-helix	148-150	3
α-helix	154-161	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exportin-1	A	protein	1071	Homo sapiens	O14980 (AlphaFold model)
GTP-binding nuclear protein Ran	B	protein	216	Homo sapiens	P62826 (AlphaFold model)
Nuclear cap-binding protein subunit 1	C	protein	790	Homo sapiens	Q09161 (AlphaFold model)
Nuclear cap-binding protein subunit 2	D	protein	156	Homo sapiens	P52298 (AlphaFold model)
Phosphorylated adapter RNA export protein	N, P	protein	394	Homo sapiens	Q9H814
RNA (5'-d((adm))-r(pa)-3')	R	RNA	14	Homo sapiens

Sequence of entity 1 (A), FASTA

>9HFL_1 Exportin-1 (chains A)
MPAIMTMLADHAARQLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHPDAW
TRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCV
EKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFD
FSSGQITQVKSKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGY
IFETKLISTLIYKFLNVPMFRNVSLKCLTEIAGVSVSQYEEQFVTLFTLTMMQLKQMLPL
NTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHDQLIEKRLNLRETLMEALHYMLLVSEV
EETEIFKICLEYWNHLAAELYRESPFSTSASPLLSGSQHFDVPPRRQLYLPMLFKVRLLM
VSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYVDTERIMTEKL
HNQVNGTEWSWKNLNTLCWAIGSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNKAII
ASNIMYIVGQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRHFV
QVQVGEVMPFIDEILNNINTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKYMLL
PNQVWDSIIQQATKNVDILKDPETVKQLGSILKTNVRACKAVGHPFVIQLGRIYLDMLNV
YKCLSENISAAIQANGEMVTKQPLIRSMRTVKRETLKLISGWVSRSNDPQMVAENFVPPL
LDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMINKDFEE
YPEHRTNFFLLLQAVNSHCFPAFLAIPPTQFKLVLDSIIWAFKHTMRNVADTGLQILFTL
LQNVAQEEAAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKIST
SLNPGNPVNNQIFLQEYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDFLV
QIKEFAGEDTSDLFLEEREIALRQADEEKHKRQMSVPGIFNPHEIPEEMCD

Sequence of entity 2 (B), FASTA

>9HFL_2 GTP-binding nuclear protein Ran (chains B)
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Sequence of entity 3 (C), FASTA

>9HFL_3 Nuclear cap-binding protein subunit 1 (chains C)
MSRRRHSDENDGGQPHKRRKTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEAD
LPNYKSKILRLLCTVARLLPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANN
YNEAVYLVRFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWV
GKELYEKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLK
KDRWQERHILRPYLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEG
PVMPGSHSVERFVIEENLHCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELF
QLPAPPHIDVMYTTLLIELCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHH
LSNFQFRWSWEDWSDCLSQDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPAN
PTCIYKYGDESSNSLPGHSVALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFN
PLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQM
IAVLVDKMIRTQIVDCAAVANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELE
EAKEKLARQHKRRSDDDDRSSDRKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMI
LTEHLVRCETDGTSVLTPWYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILA
VFQQFCALQA

Sequence of entity 4 (D), FASTA

>9HFL_4 Nuclear cap-binding protein subunit 2 (chains D)
MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELF
SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK
EGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ

Sequence of entity 5 (N, P), FASTA

>9HFL_5 Phosphorylated adapter RNA export protein (chains N, P)
MALEVGDMEDGQLSDSDSDMTVAPSDRPLQLPKVLGGDSAMRAFQNTATACAPVSHYRAV
ESVDSSEESFSDSDDDSCLWKRKRQKCFNPPPKPEPFQFGQSSQKPPVAGGKKINNIWGA
VLQEQNQDAVATELGILGMEGTIDRSRQSETYNYLLAKKLRKESQEHTKDLDKELDEYMH
GGKKMGSKEEENGQGHLKRKRPVKDRLGNRPEMNYKGRYEITAEDSQEKVADEISFRLQE
PKKDLIARVVRIIGNKKAIELLMETAEVEQNGGLFIMNGSRRRTPGGVFLNLLKNTPSIS
EEQIKDIFYIENQKEYENKKAARKRRTQVLGKKMKQAIKSLNFQEDDDTSRETFASDTNE
ALASLDESQEGHAEAKLEAEEAIEVDHSHDLDIF

Sequence of entity 6 (R), FASTA

>9HFL_6 RNA (5'-D(*(ADM))-R(P*A)-3') (chains R)
AAUCUAUAAUAGCA

Ligands and cofactors

ID	Name	Formula	Copies
GTA	P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate	C21 H30 N10 O17 P3	1
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

Structural basis for the synergistic assembly of the snRNA export complex. Dubiez, E., Garland, W., Finderup Brask, M. et al. Nat Struct Mol Biol (2025) 32:1555-1566. DOI 10.1038/s41594-025-01595-5 · 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
9OGD 2.49 Å, Cryo-EM structure of human exportin-1 conjugated with selinexor and bound to human…
7B51 2.58 Å, Crystal structure of human CRM1 covalently modified by 2-mercaptoethanol at Cys528
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

Browse structure collections

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