3NC0: HIV-1 Rev NES-CRM1-RanGTP nuclear export complex

Crystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal II). Determined by X-ray diffraction at 2.9 Å resolution. Released 27 Oct 2010.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 25,190
Mol. weight: 373.37 kDa
Ligands: MG, GTP, IPH
Released: 27 Oct 2010

Explore 3NC0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NC0 contains 165 α-helices and 52 β-strands across 6 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, 4 β-strands

Element	Residues	Length	Sheet
α-helix	27-34	8
α-helix	39-48	10
α-helix	58-65	8
α-helix	73-89	17
α-helix	91-93	3
α-helix	96-114	19
α-helix	124-145	22
α-helix	149-159	11
α-helix	162-175	14
α-helix	176-180	5
β-strand	183	1	1
β-strand	186	1	1
α-helix	188-200	13
α-helix	202-215	14
α-helix	219-230	12
α-helix	239-242	4
α-helix	246-249	4
α-helix	250-254	5
α-helix	258-260	3
α-helix	261-271	11
α-helix	280-297	18
α-helix	304-309	6
α-helix	315-339	25
α-helix	346-357	12
α-helix	363-379	17
α-helix	387-388	2
α-helix	392-393	2
α-helix	406-423	18
α-helix	424-426	3
β-strand	430-432	3	2
β-strand	442-444	3	2
α-helix	449-467	19
α-helix	469-484	16
α-helix	491-503	13
α-helix	510-530	21
α-helix	534-550	17
α-helix	552-555	4
α-helix	559-572	14
α-helix	580-595	16
α-helix	596-599	4
α-helix	602-603	2
α-helix	610-615	6
α-helix	618-622	5
α-helix	627-641	15
α-helix	647-657	11
α-helix	659-672	14
α-helix	678-680	3
α-helix	682-702	21
α-helix	704-706	3
α-helix	707-735	29
α-helix	737-740	4
α-helix	743-764	22
α-helix	769-775	7
α-helix	778-780	3
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	819-831	13
α-helix	842-858	17
α-helix	862-865	4
α-helix	868-881	14
α-helix	887-906	20
α-helix	908-930	23
α-helix	936-938	3
α-helix	939-953	15
α-helix	970-985	16
α-helix	991-1003	13
α-helix	1008-1022	15
α-helix	1035-1041	7
α-helix	1043-1046	4

Chain B: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	20	1	3
α-helix	42-50	9
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
β-strand	228-231	4	4
α-helix	232-233	2
β-strand	235-236	2	3
α-helix	239-245	7
β-strand	254-261	8	3
β-strand	269-277	9	3
α-helix	279-282	4

Chain C: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	5
α-helix	23-32	10
α-helix	41-43	3
β-strand	45-54	10	5
β-strand	57-66	10	5
α-helix	77-79	3
β-strand	85-91	7	5
α-helix	96-99	4
α-helix	101-109	9
β-strand	117-122	6	5
α-helix	133-135	3
α-helix	138-142	5
β-strand	145-148	4	5
β-strand	150	1	6
β-strand	155	1	6
α-helix	159-168	10
β-strand	176	1	5

Chain D: 66 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	27-34	8
α-helix	39-48	10
α-helix	58-65	8
α-helix	73-89	17
α-helix	91-93	3
α-helix	96-113	18
α-helix	124-145	22
α-helix	149-159	11
α-helix	162-175	14
α-helix	176-180	5
β-strand	183	1	7
β-strand	186	1	7
α-helix	188-200	13
α-helix	202-215	14
α-helix	219-230	12
α-helix	239-242	4
α-helix	246-249	4
α-helix	250-254	5
α-helix	258-260	3
α-helix	261-271	11
α-helix	280-297	18
α-helix	304-309	6
α-helix	315-333	19
α-helix	336-339	4
α-helix	346-357	12
α-helix	363-379	17
α-helix	387-388	2
α-helix	406-423	18
α-helix	424-426	3
β-strand	430-434	5	8
β-strand	440-444	5	8
α-helix	449-467	19
α-helix	469-484	16
α-helix	491-503	13
α-helix	510-530	21
α-helix	534-550	17
α-helix	552-555	4
α-helix	559-572	14
α-helix	580-600	21
α-helix	602-603	2
α-helix	610-615	6
α-helix	618-622	5
α-helix	627-641	15
α-helix	647-657	11
α-helix	659-672	14
α-helix	676-680	5
α-helix	682-702	21
α-helix	704-706	3
α-helix	707-735	29
α-helix	737-740	4
α-helix	743-765	23
α-helix	769-775	7
α-helix	778-780	3
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	819-831	13
α-helix	842-858	17
α-helix	862-865	4
α-helix	868-882	15
α-helix	887-906	20
α-helix	908-930	23
α-helix	936-938	3
α-helix	939-953	15
α-helix	970-985	16
α-helix	991-1003	13
α-helix	1008-1023	16
α-helix	1035-1051	17

Chain E: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	20	1	9
α-helix	42-50	9
α-helix	58-67	10
β-strand	103-107	5	9
α-helix	115-118	4
β-strand	119-125	7	9
β-strand	128-135	8	10
β-strand	138-142	5	10
β-strand	148-152	5	10
β-strand	170-177	8	10
β-strand	182-191	10	10
β-strand	194-195	2	10
α-helix	201-211	11
β-strand	228-231	4	10
α-helix	232-233	2
β-strand	235-236	2	9
α-helix	239-245	7
β-strand	254-261	8	9
β-strand	269-277	9	9
α-helix	281-285	5

Chain F: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	11
α-helix	23-31	9
α-helix	41-43	3
β-strand	45-54	10	11
β-strand	57-66	10	11
β-strand	85-91	7	11
α-helix	96-99	4
α-helix	101-109	9
β-strand	117-122	6	11
α-helix	133-135	3
α-helix	138-142	5
β-strand	145-148	4	11
β-strand	150	1	12
β-strand	155	1	12
α-helix	159-168	10
β-strand	176	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exportin-1	A, D	protein	1073	Mus musculus	Q6P5F9 (AlphaFold model)
Snurportin-1	B, E	protein	362	Homo sapiens	O95149 (AlphaFold model)
GTP-binding nuclear protein Ran	C, F	protein	176	Homo sapiens	P62826 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>3NC0_1 Exportin-1 (chains A, D)
GSMPAIMTMLADHAARQLLDFSQKLDINLLDNVVNCLYHGEGAQQRMAQEVLTHLKEHPD
AWTRVDTILEFSQNMNTKYYGLQILENVIKTRWKILPRNQCEGIKKYVVGLIIKTSSDPT
CVEKEKVYIGKLNMILVQILKQEWPKHWPTFISDIVGASRTSESLCQNNMVILKLLSEEV
FDFSSGQITQVKAKHLKDSMCNEFSQIFQLCQFVMENSQNAPLVHATLETLLRFLNWIPL
GYIFETKLISTLIYKFLNVPMFRNVSLKCLTEIAGVSVSQYEEQFETLFTLTMMQLKQML
PLNTNIRLAYSNGKDDEQNFIQNLSLFLCTFLKEHGQLLEKRLNLREALMEALHYMLLVS
EVEETEIFKICLEYWNHLAAELYRESPFSTSASPLLSGSQHFDIPPRRQLYLTVLSKVRL
LMVSRMAKPEEVLVVENDQGEVVREFMKDTDSINLYKNMRETLVYLTHLDYVDTEIIMTK
KLQNQVNGTEWSWKNLNTLCWAIGSISGAMHEEDEKRFLVTVIKDLLGLCEQKRGKDNKA
IIASNIMYIVGQYPRFLRAHWKFLKTVVNKLFEFMHETHDGVQDMACDTFIKIAQKCRRH
FVQVQVGEVMPFIDEILNNINTIICDLQPQQVHTFYEAVGYMIGAQTDQTVQEHLIEKYM
LLPNQVWDSIIQQATKNVDILKDPETVKQLGSILKTNVRACKAVGHPFVIQLGRIYLDML
NVYKCLSENISAAIQANGEMVTKQPLIRSMRTVKRETLKLISGWVSRSNDPQMVAENFVP
PLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMINKDF
EEYPEHRTNFFLLLQAVNSHCFPAFLAIPPAQFKLVLDSIIWAFKHTMRNVADTGLQILF
TLLQNVAQEEAAAQSFYQTYFCDILQHIFSVVTDTSHTAGLTMHASILAYMFNLVEEGKI
STPLNPGNPVNNQMFIQDYVANLLKSAFPHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDF
LVQIKEFAGEDTSDLFLEERETALRQAQEEKHKLQMSVPGILNPHEIPEEMCD

Sequence of entity 2 (B, E), FASTA

>3NC0_2 Snurportin-1 (chains B, E)
GSPVPLQLPPLERLTLSQDLNSTAAPHPRLSQYKSKYSSLEQSERRRRLLELQKSKRLDY
VNHARRLAEDDWTGMESEEENKKDDEEMDIDTVKKLPKHYANQLMLSEWLIDVPSDLGQE
WIVVVCPVGKRALIVASRGSTSAYTKSGYCVNRFSSLLPGGNRRNSTAKDYTILDCIYNE
VNQTYYVLDVMCWRGHPFYDCQTDFRFYWMHSKLPEEEGLGEKTKLNPFKFVGLKNFPCT
PESLCDVLSMDFPFEVDGLLFYHKQTHYSPGSTPLVGWLRPYMVSDVLGVAVPAGPLTTK
PDYAGHQLQQIMEHKKSQKEGMKEKLTHKASENGHYELEHLSTPKLKGSSHSPDHPGCLM
EN

Sequence of entity 3 (C, F), FASTA

>3NC0_3 GTP-binding nuclear protein Ran (chains C, F)
GEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVW
DTAGLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKV
DIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
IPH	Phenol	C6 H6 O	1

Water and common crystallization additives (PEG, GOL) are not listed.

Primary citation

NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1. Guttler, T., Madl, T., Neumann, P. et al. Nat Struct Mol Biol (2010) 17:1367-1376. DOI 10.1038/nsmb.1931 · PubMed

Other PDB entries of the same protein (UniProt Q6P5F9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3GJX 2.5 Å, Crystal Structure of the Nuclear Export Complex CRM1-Snurportin1-RanGTP
3NBZ 2.8 Å, Crystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal I)
3NC1 3.35 Å, Crystal structure of the CRM1-RanGTP complex
3NBY 3.42 Å, Crystal structure of the PKI NES-CRM1-RanGTP nuclear export complex

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