5DIS: CRM1-RanGTP-SPN1 export complex

Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino acid FG-repeat containing fragment of Nup214. Determined by X-ray diffraction at 2.85 Å resolution. Released 4 Nov 2015.

Method: X-ray diffraction
Resolution: 2.85 Å
Organisms: Homo sapiens, Escherichia coli (strain K12)
Chains: 4
Atoms: 14,991
Mol. weight: 225.18 kDa
Ligands: PRO, GTP, MG
Released: 4 Nov 2015

Explore 5DIS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DIS contains 111 α-helices and 38 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: 69 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
α-helix	25-37	13
α-helix	40-55	16
α-helix	60-69	10
α-helix	73-90	18
α-helix	91-93	3
α-helix	96-114	19
α-helix	117-119	3
α-helix	124-141	18
α-helix	149-156	8
α-helix	161-175	15
α-helix	176-180	5
α-helix	188-200	13
α-helix	202-215	14
α-helix	219-235	17
α-helix	239-242	4
α-helix	246-253	8
α-helix	258-273	16
α-helix	277-279	3
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	404-423	20
α-helix	424-426	3
β-strand	429-434	6	1
β-strand	440-445	6	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	602-603	2
α-helix	610-616	7
α-helix	618-622	5
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	738-741	4
α-helix	743-764	22
α-helix	769-771	3
α-helix	772-776	5
α-helix	777-780	4
α-helix	781-785	5
α-helix	786-790	5
α-helix	793-795	3
α-helix	799-811	13
α-helix	812-814	3
α-helix	816-818	3
α-helix	819-831	13
α-helix	842-858	17
α-helix	861-864	4
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	1035-1047	13

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	2
α-helix	23-31	9
β-strand	45-54	10	2
β-strand	57-66	10	2
α-helix	70-72	3
α-helix	76-80	5
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
β-strand	145-148	4	2
α-helix	159-169	11
β-strand	176-177	2	2

Chain C: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	0-10	11
β-strand	20	1	3
α-helix	24-25	2
α-helix	40-51	12
α-helix	58-67	10
β-strand	103-107	5	3
α-helix	115-118	4
β-strand	119-125	7	3
β-strand	128-135	8	4
β-strand	138-142	5	4
β-strand	148-152	5	4
β-strand	170-177	8	4
β-strand	182-191	10	4
β-strand	194-195	2	4
α-helix	201-211	11
α-helix	213-219	7
β-strand	228-231	4	4
α-helix	232-233	2
β-strand	234-236	3	3
α-helix	239-247	9
β-strand	254-261	8	3
β-strand	269-277	9	3
α-helix	279-284	6

Chain D: 24 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	5
α-helix	19-31	13
β-strand	35-38	4	5
α-helix	43-50	8
α-helix	51-53	3
β-strand	59-62	4	5
α-helix	67-73	7
β-strand	76	1	6
β-strand	89	1	7
α-helix	91-97	7
β-strand	98-99	2	8
β-strand	102-103	2	8
β-strand	105-110	6	5
α-helix	125-126	2
α-helix	133-135	3
α-helix	136-141	6
α-helix	154-157	4
α-helix	161-164	4
β-strand	170-171	2	9
β-strand	176-177	2	9
α-helix	188-200	13
α-helix	214-218	5
α-helix	229-231	3
β-strand	258-259	2	10
β-strand	262-266	5	5
β-strand	267	1	6
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	5
β-strand	304	1	7
α-helix	305-308	4
α-helix	315-325	11
β-strand	328-329	2	10
α-helix	330-331	2
α-helix	336-352	17
α-helix	358-366	9
α-helix	1925-1929	5
α-helix	1985-1987	3
α-helix	2016-2019	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exportin-1	A	protein	1044	Homo sapiens	O14980 (AlphaFold model)
GTP-binding nuclear protein Ran	B	protein	172	Homo sapiens	P62826 (AlphaFold model)
Snurportin-1	C	protein	289	Homo sapiens	O95149 (AlphaFold model)
Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214	D	protein	479	Escherichia coli (strain K12), Homo sapiens	P0AEX9 (AlphaFold model), P35658

Sequence of entity 1 (A), FASTA

>5DIS_1 Exportin-1 (chains A)
MTMLADHAARQLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHPDAWTRVD
TILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPTCVEKEK
VYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEVFDFSSG
QITQVKSKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPLGYIFET
KLISTLIYKFLNVPMFRNVSLKCLTEIAGVSVSQYEEQFVTLFTLTMMQLKQMLPLNTNI
RLAYSNGKDDEQNFIQNLSLFLCTFLKEHDQLIEKRLNLRETLMEALHYMLLVSEVEETE
IFKICLEYWNHLAAELYRESPFSTSASPLLSGSQHFDVPPRRQLYLPMLFKVRLLMVSRM
AKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYVDTERIMTEKLHNQV
NGTEWSWKNLNTLCWAIGSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNKAIIASNI
MYIVGQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRHFVQVQV
GEVMPFIDEILNNINTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKYMLLPNQV
WDSIIQQATKNVDILKDPETVKQLGSILKTNVRACKAVGHPFVIQLGRIYLDMLNVYKCL
SENISAAIQANGEMVTKQPLIRSMRTVKRETLKLISGWVSRSNDPQMVAENFVPPLLDAV
LIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMINKDFEEYPEH
RTNFFLLLQAVNSHCFPAFLAIPPTQFKLVLDSIIWAFKHTMRNVADTGLQILFTLLQNV
AQEEAAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKISTSLNP
GNPVNNQIFLQEYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDFLVQIKE
FAGEDTSDLFLEEREIALRQADEE

Sequence of entity 2 (B), FASTA

>5DIS_2 GTP-binding nuclear protein Ran (chains B)
QVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTA
GLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIK
DRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAM

Sequence of entity 3 (C), FASTA

>5DIS_3 Snurportin-1 (chains C)
GSMEELSQALASSFSVSQDLNSTAAPHPRLSQYKSKYSSLEQSERRRRLLELQKSKRLDY
VNHARRLAEDDWTGMESEEENKKDDEEMDIDTVKKLPKHYANQLMLSEWLIDVPSDLGQE
WIVVVCPVGKRALIVASRGSTSAYTKSGYCVNRFSSLLPGGNRRNSTAKDYTILDCIYNE
VNQTYYVLDVMCWRGHPFYDCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCT
PESLCDVLSMDFPFEVDGLLFYHKQTHYSPGSTPLVGWLRPYMVSDVLG

Sequence of entity 4 (D), FASTA

>5DIS_4 Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214 (chains D)
KLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHD
RFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNP
PKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDN
AGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVT
VLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALK
SYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALAAAQ
TNAAAEFSNTSNLFGNSGAKTFGGFASSSFGEQKPTGTFSSGGGSVASQGFGFSSPNKTG
GFGAAPVFGSPPTFGGSPGFGGVPAFGSAPAFTSPLGSTGGKVFGEGTAAASAGGFGFG

Ligands and cofactors

ID	Name	Formula	Copies
PRO	Proline	C5 H9 N O2	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1

Primary citation

Structural and Functional Characterization of CRM1-Nup214 Interactions Reveals Multiple FG-Binding Sites Involved in Nuclear Export. Port, S.A., Monecke, T., Dickmanns, A. et al. Cell Rep (2015) 13:690-702. DOI 10.1016/j.celrep.2015.09.042 · 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…
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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