3FEX: CBC-importin alpha complex

Crystal structure of the CBC-importin alpha complex. Determined by X-ray diffraction at 3.55 Å resolution. Released 11 Aug 2009.

Method: X-ray diffraction
Resolution: 3.55 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,051
Mol. weight: 160.77 kDa
Released: 11 Aug 2009

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

Secondary structure: helices and β-sheets

3FEX contains 84 α-helices and 10 β-strands across 3 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: 50 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	5-6	2
α-helix	25-37	13
α-helix	46-58	13
α-helix	61-78	18
α-helix	80-82	3
α-helix	83-96	14
α-helix	98-117	20
α-helix	121-133	13
α-helix	135-137	3
β-strand	140	1	1
α-helix	142-150	9
α-helix	153-157	5
α-helix	163-174	12
α-helix	177-187	11
α-helix	189-205	17
α-helix	211-214	4
β-strand	227	1	2
α-helix	230-241	12
α-helix	252-255	4
α-helix	257-262	6
β-strand	266	1	1
α-helix	282-285	4
β-strand	287	1	2
α-helix	294-296	3
α-helix	302-305	4
α-helix	309-325	17
α-helix	329-337	9
α-helix	347-359	13
α-helix	369-382	14
α-helix	387-400	14
α-helix	402-404	3
α-helix	407-421	15
α-helix	430-436	7
α-helix	444-459	16
α-helix	462-468	7
α-helix	473-475	3
α-helix	478-479	2
α-helix	498-509	12
α-helix	514-521	8
α-helix	541-554	14
α-helix	559-568	10
α-helix	570-576	7
α-helix	580-593	14
α-helix	598-607	10
α-helix	616-623	8
α-helix	626-628	3
α-helix	641-664	24
α-helix	684-731	48
α-helix	738-753	16
α-helix	755-758	4
α-helix	762-764	3
α-helix	765-769	5
α-helix	776-786	11
α-helix	787-789	3

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
β-strand	41-45	5	3
α-helix	53-60	8
α-helix	61-63	3
β-strand	66-71	6	3
β-strand	83-88	6	3
α-helix	91-99	9
β-strand	105-106	2	4
β-strand	109-110	2	4
β-strand	112-115	4	3

Chain C: 30 helices, 0 β-strands

Element	Residues	Length
α-helix	78-85	8
α-helix	90-103	14
α-helix	112-116	5
α-helix	120-128	9
α-helix	134-145	12
α-helix	152-160	9
α-helix	163-170	8
α-helix	176-190	15
α-helix	194-202	9
α-helix	206-211	6
α-helix	223-234	12
α-helix	247-250	4
α-helix	253-258	6
α-helix	265-278	14
α-helix	283-290	8
α-helix	295-302	8
α-helix	307-320	14
α-helix	326-333	8
α-helix	336-338	3
α-helix	340-344	5
α-helix	349-363	15
α-helix	367-375	9
α-helix	379-387	9
α-helix	391-407	17
α-helix	410-418	9
α-helix	422-426	5
α-helix	434-452	19
α-helix	457-466	10
α-helix	469-474	6
α-helix	482-495	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear cap-binding protein subunit 1	A	protein	790	Homo sapiens	Q09161 (AlphaFold model)
Nuclear cap-binding protein subunit 2	B	protein	156	Homo sapiens	P52298 (AlphaFold model)
Importin subunit alpha-2	C	protein	467	Homo sapiens	P52292 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3FEX_1 Nuclear cap-binding protein subunit 1 (chains A)
MSRRRHSDENDGGQPHKRRKTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEAD
LPNYKSKILRLLCTVARLLPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANN
YNEAVYLVRFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWV
GKELYEKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLK
KDRWQERHILRPYLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEG
PVMPGSHSVERFVIEENLHCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELF
QLPAPPHIDVMYTTLLIELCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHH
LSNFQFRWSWEDWSDCLSQDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPAN
PTCIYKYGDESSNSLPGHSVALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFN
PLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQM
IAVLVDKMIRTQIVDCAAVANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELE
EAKEKLARQHKRRSDDDDRSSDRKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMI
LTEHLVRCETDGTSVLTPWYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILA
VFQQFCALQA

Sequence of entity 2 (B), FASTA

>3FEX_2 Nuclear cap-binding protein subunit 2 (chains B)
MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELF
SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK
EGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ

Sequence of entity 3 (C), FASTA

>3FEX_3 Importin subunit alpha-2 (chains C)
MNQGTVNWSVDDIVKGINSSNVENQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFL
GRTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGN
IAGDGSVFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPIDA
VEQILPTLVRLLHHDDPEVLADTCWAISYLTDGPNERIGMVVKTGVVPQLVKLLGASELP
IVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQD
QIQQVVNHGLVPFLVSVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCGIIEPLMNL
LTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKAS
LSLIEKYFSVEEEEDQNVVPETTSEGYTFQVQDGAPGTFNFHHHHHH

Primary citation

The molecular basis for the regulation of the cap-binding complex by the importins. Dias, S.M., Wilson, K.F., Rojas, K.S. et al. Nat Struct Mol Biol (2009) 16:930-937. DOI 10.1038/nsmb.1649 · PubMed

Other PDB entries of the same protein (UniProt Q09161 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1H2V 2.0 Å, Structure of the human nuclear cap-binding-complex (CBC)
1H6K 2.0 Å, nuclear Cap Binding Complex
1H2T 2.1 Å, Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue…
1N52 2.11 Å, Cap Binding Complex
3FEY 2.2 Å, Crystal structure of the CBC-importin alpha complex.
1H2U 2.4 Å, Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue…
9HFL 2.62 Å, Cryo-EM structure of the human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and…
6D0Y 2.68 Å, X-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP80-CBP20 Cap Binding…
1N54 2.72 Å, Cap Binding Complex m7GpppG free
5OOB 2.79 Å, Complex of human nuclear cap-binding complex with M7GTP and nelf-E C-terminal peptide
5OO6 2.8 Å, Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide
8BY6 3.19 Å, Structure of the human nuclear cap-binding complex bound to NCBP3(560-620) and…

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