9B62: Exportin-1

Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model. Determined by electron microscopy at 2.9 Å resolution. Released 16 Oct 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 7
Atoms: 19,287
Mol. weight: 337.26 kDa
Ligands: GTP, MG
Released: 16 Oct 2024

Explore 9B62 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B62 contains 129 α-helices and 57 β-strands across 7 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: 70 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	15-17	3
α-helix	25-36	12
α-helix	41-54	14
α-helix	59-62	4
α-helix	63-69	7
α-helix	73-90	18
α-helix	91-93	3
α-helix	96-114	19
α-helix	117-122	6
α-helix	126-145	20
α-helix	149-156	8
α-helix	161-175	15
α-helix	176-180	5
α-helix	188-200	13
α-helix	207-215	9
α-helix	219-232	14
α-helix	239-242	4
α-helix	246-249	4
α-helix	250-254	5
α-helix	258-260	3
α-helix	261-272	12
α-helix	281-294	14
α-helix	304-309	6
α-helix	313-339	27
α-helix	344-357	14
α-helix	363-383	21
α-helix	387-388	2
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	469-484	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	597-600	4
α-helix	610-616	7
α-helix	627-641	15
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	769-775	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	812-815	4
α-helix	819-822	4
α-helix	823-827	5
α-helix	828-834	7
α-helix	842-858	17
α-helix	860-864	5
α-helix	868-881	14
α-helix	887-906	20
α-helix	908-930	23
α-helix	933-938	6
α-helix	939-954	16
α-helix	970-985	16
α-helix	991-1003	13
α-helix	1008-1021	14
α-helix	1035-1051	17

Chain B: 8 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	101-109	9
β-strand	117-122	6	2
α-helix	133-135	3
α-helix	138-142	5
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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
β-strand	25-30	6	4
α-helix	31	1
β-strand	36-46	11	4
α-helix	47-48	2
β-strand	57-63	7	4
α-helix	72-73	2
β-strand	74-77	4	4
α-helix	80-81	2
β-strand	86	1	5
β-strand	91	1	4
β-strand	92	1	5
β-strand	94	1	6
α-helix	109-120	12
α-helix	131-139	9
α-helix	141-154	14

Chain D: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	7
β-strand	33-38	6	7
α-helix	45-54	10
β-strand	62-65	4	7
β-strand	70	1	7
α-helix	77-80	4
β-strand	86-92	7	7
β-strand	96	1	6

Chain E: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2510-2512	3
β-strand	2633-2637	5	7
α-helix	2642-2651	10
α-helix	2657-2662	6
α-helix	2677-2684	8
α-helix	2850-2856	7
α-helix	2912-2914	3
β-strand	2930-2944	15	8
β-strand	2949-2963	15	8
β-strand	2969-2975	7	8
β-strand	2981-2986	6	8
β-strand	2994-2995	2	8
β-strand	3002-3009	8	8
β-strand	3016-3023	8	8
α-helix	3027-3047	21

Chain F: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	9
α-helix	23-31	9
β-strand	45-54	10	9
β-strand	57-66	10	9
α-helix	74-76	3
α-helix	77-80	4
β-strand	85-91	7	9
α-helix	95-98	4
α-helix	101-111	11
β-strand	117-122	6	9
α-helix	138-141	4
β-strand	145-148	4	9
β-strand	150	1	10
β-strand	155	1	10
α-helix	159-169	11
β-strand	176	1	9
α-helix	191-204	14

Chain G: 26 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
β-strand	23-24	2	11
β-strand	31-32	2	12
α-helix	36-38	3
α-helix	39-46	8
β-strand	54-55	2	11
β-strand	60-61	2	12
α-helix	63-73	11
β-strand	81-83	3	11
β-strand	88	1	12
α-helix	96-110	15
β-strand	116-118	3	11
α-helix	125-137	13
α-helix	139-141	3
β-strand	146-148	3	11
α-helix	155-176	22
β-strand	184-186	3	11
α-helix	195-206	12
β-strand	212-214	3	11
α-helix	222-234	13
β-strand	240-242	3	11
α-helix	251-262	12
β-strand	268-270	3	11
α-helix	280-289	10
β-strand	297-299	3	11
α-helix	307-318	12
β-strand	325-327	3	11
α-helix	335-346	12
β-strand	354	1	11
α-helix	355-356	2
α-helix	434-439	6
α-helix	443-448	6
α-helix	450-452	3
α-helix	453-460	8
α-helix	466-478	13
α-helix	484-502	19
α-helix	509-520	12
α-helix	536-546	11
α-helix	556-563	8
α-helix	568-571	4
α-helix	574-586	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exportin-1	A	protein	1074	Homo sapiens	O14980 (AlphaFold model)
GTP-binding nuclear protein Ran	B, F	protein	222	Homo sapiens	P62826 (AlphaFold model)
SUMO-conjugating enzyme UBC9	C	protein	161	Homo sapiens	P63279 (AlphaFold model)
Small ubiquitin-related modifier 1	D	protein	101	Homo sapiens	P63165 (AlphaFold model)
E3 SUMO-protein ligase RanBP2	E	protein	619	Homo sapiens	P49792
Ran GTPase-activating protein 1	G	protein	591	Homo sapiens	P46060

Sequence of entity 1 (A), FASTA

>9B62_1 Exportin-1 (chains A)
SHMMPAIMTMLADHAARQLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHP
DAWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDP
TCVEKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEE
VFDFSSGQITQVKSKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIP
LGYIFETKLISTLIYKFLNVPMFRNVSLKCLTEIAGVSVSQYEEQFVTLFTLTMMQLKQM
LPLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHDQLIEKRLNLRETLMEALHYMLLV
SEVEETEIFKICLEYWNHLAAELYRESPFSTSASPLLSGSQHFDVPPRRQLYLPMLFKVR
LLMVSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYVDTERIMT
EKLHNQVNGTEWSWKNLNTLCWAIGSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNK
AIIASNIMYIVGQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRR
HFVQVQVGEVMPFIDEILNNINTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKY
MLLPNQVWDSIIQQATKNVDILKDPETVKQLGSILKTNVRACKAVGHPFVIQLGRIYLDM
LNVYKCLSENISAAIQANGEMVTKQPLIRSMRTVKRETLKLISGWVSRSNDPQMVAENFV
PPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMINKD
FEEYPEHRTNFFLLLQAVNSHCFPAFLAIPPTQFKLVLDSIIWAFKHTMRNVADTGLQIL
FTLLQNVAQEEAAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGK
ISTSLNPGNPVNNQIFLQEYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRD
FLVQIKEFAGEDTSDLFLEEREIALRQADEEKHKRQMSVPGIFNPHEIPEEMCD

Sequence of entity 2 (B, F), FASTA

>9B62_2 GTP-binding nuclear protein Ran (chains B, F)
GSHMASMAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHT
NRGPIKFNVWDTAGLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCEN
IPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNL
EFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Sequence of entity 3 (C), FASTA

>9B62_3 SUMO-conjugating enzyme UBC9 (chains C)
GSHMSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGL
FKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQ
ELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS

Sequence of entity 4 (D), FASTA

>9B62_4 Small ubiquitin-related modifier 1 (chains D)
GSHMMSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQG
VPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEPTGG

Sequence of entity 5 (E), FASTA

>9B62_5 E3 SUMO-protein ligase RanBP2 (chains E)
GSHMDSLITPHVSRSSTPRESPCGKIAVAVLEETTRERTDVIQGDDVADATSEVEVSSTS
ETTPKAVVSPPKFVFGSESVKSIFSSEKSKPFAFGNSSATGSLFGFSFNAPLKSNNSETS
SVAQSGSESKVEPKKCELSKNSDIEQSSDSKVKNLFASFPTEESSINYTFKTPEKAKEKK
KPEDSPSDDDVLIVYELTPTAEQKALATKLKLPPTFFCYKNRPDYVSEEEEDDEDFETAV
KKLNGKLYLDGSEKCRPLEENTADNEKECIIVWEKKPTVEEKAKADTLKLPPTFFCGVCS
DTDEDNGNGEDFQSELQKVQEAQKSQTEEITSTTDSVYTGGTEVMVPSFCKSEEPDSITK
SISSPSVSSETMDKPVDLSTRKEIDTDSTSQGESKIVSFGFGSSTGLSFADLASSNSGDF
AFGSKDKNFQWANTGAAVFGTQSVGTQSAGKVGEDEDGSDEEVVHNEDIHFEPIVSLPEV
EVKSGEEDEEILFKERAKLYRWDRDVSQWKERGVGDIKILWHTMKNYYRILMRRDQVFKV
CANHVITKTMELKPLNVSNNALVWTASDYADGEAKVEQLAVRFKTKEVADCFKKTFEECQ
QNLMKLQKGHVSLAAELSK

Sequence of entity 6 (G), FASTA

>9B62_6 Ran GTPase-activating protein 1 (chains G)
GSHMMASEDIAKLAETLAKTQVAGGQLSFKGKSLKLNTAEDAKDVIKEIEDFDSLEALRL
EGNTVGVEAARVIAKALEKKSELKRCHWSDMFTGRLRTEIPPALISLGEGLITAGAQLVE
LDLSDNAFGPDGVQGFEALLKSSACFTLQELKLNNCGMGIGGGKILAAALTECHRKSSAQ
GKPLALKVFVAGRNRLENDGATALAEAFRVIGTLEEVHMPQNGINHPGITALAQAFAVNP
LLRVINLNDNTFTEKGAVAMAETLKTLRQVEVINFGDCLVRSKGAVAIADAIRGGLPKLK
ELNLSFCEIKRDAALAVAEAMADKAELEKLDLNGNTLGEEGCEQLQEVLEGFNMAKVLAS
LSDDEDEEEEEEGEEEEEEAEEEEEEDEEEEEEEEEEEEEEPQQRGQGEKSATPSRKILD
PNTGEPAPVLSSPPPADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLKV
SSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANLY
GPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESCSFARHSLLQTLYKV

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Structural basis for a nucleoporin exportin complex between RanBP2, SUMO1-RanGAP1, the E2 Ubc9, Crm1 and the Ran GTPase. Baytshtok, V., DiMattia, M.A., Lima, C.D. Nat Commun (2025) 16:6403-6403. DOI 10.1038/s41467-025-61694-1 · 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
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
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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