5H2W: Karyopherin Kap60p

Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-340). Determined by X-ray diffraction at 2.5 Å resolution. Released 14 Dec 2016.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 6,752
Mol. weight: 137.94 kDa
Released: 14 Dec 2016

Explore 5H2W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5H2W contains 69 α-helices and 0 β-strands across 2 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: 34 helices, 0 β-strands

Element	Residues	Length
α-helix	90-96	7
α-helix	101-115	15
α-helix	123-128	6
α-helix	132-137	6
α-helix	145-159	15
α-helix	163-171	9
α-helix	175-184	10
α-helix	187-201	15
α-helix	205-213	9
α-helix	217-222	6
α-helix	223-225	3
α-helix	229-243	15
α-helix	249-250	2
α-helix	252-255	4
α-helix	256-258	3
α-helix	259-265	7
α-helix	271-284	14
α-helix	289-297	9
α-helix	301-307	7
α-helix	313-326	14
α-helix	331-339	9
α-helix	342-349	8
α-helix	355-368	14
α-helix	373-381	9
α-helix	385-394	10
α-helix	397-411	15
α-helix	412-414	3
α-helix	419-426	8
α-helix	430-436	7
α-helix	442-464	23
α-helix	472-479	8
α-helix	482-488	7
α-helix	489-491	3
α-helix	495-508	14

Chain C: 35 helices, 0 β-strands

Element	Residues	Length
α-helix	90-96	7
α-helix	101-115	15
α-helix	123-127	5
α-helix	132-137	6
α-helix	145-159	15
α-helix	163-171	9
α-helix	175-184	10
α-helix	187-201	15
α-helix	205-213	9
α-helix	217-222	6
α-helix	223-225	3
α-helix	229-242	14
α-helix	249-250	2
α-helix	252-255	4
α-helix	256-258	3
α-helix	259-265	7
α-helix	271-284	14
α-helix	289-297	9
α-helix	300-306	7
α-helix	307-309	3
α-helix	313-326	14
α-helix	331-339	9
α-helix	342-349	8
α-helix	355-368	14
α-helix	373-381	9
α-helix	385-394	10
α-helix	397-411	15
α-helix	412-414	3
α-helix	419-426	8
α-helix	430-436	7
α-helix	442-461	20
α-helix	472-479	8
α-helix	482-488	7
α-helix	489-491	3
α-helix	495-508	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Importin subunit alpha	A, C	protein	423	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q02821 (AlphaFold model)
Ubiquitin-like-specific protease 1	B, D	protein	191	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q02724 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5H2W_1 Importin subunit alpha (chains A, C)
ELPQMTQQLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEML
QLEAAWALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDY
RDYVLQCNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIY
SMDTETLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIV
TGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNITAGNTEQIQAVIDANLIPP
LVKLLEVAEYKTKKEACWAISNASSGGLQRPDIIRYLVSQGCIKPLCDLLEIADNRIIEV
TLDALENILKMGEADKEARGLNINENADFIEKAGGMEKIFNCQQNENDKIYEKAYKIIET
YFG

Sequence of entity 2 (B, D), FASTA

>5H2W_2 Ubiquitin-like-specific protease 1 (chains B, D)
SSDTRKHKFDTSTWALPNKRRRIESEGVGTPSTSPISSLASQKSNCDSDNSITFSRDPFG
WNKWKTSAIGSNSENNTSDQKNSYDRRQYGTAFIRKKKVAKQNINNTKLVSRAQSEEVTY
LRQIFNGEYKVPKILKEERERQLKLMDMDKEKDTGLKKSIIDLTEKIKTILIENNKNRLQ
TRNENDDDLVF

Primary citation

Structures of the Karyopherins Kap121p and Kap60p Bound to the Nuclear Pore-Targeting Domain of the SUMO Protease Ulp1p. Hirano, H., Kobayashi, J., Matsuura, Y. J Mol Biol (2017) 429:249-260. DOI 10.1016/j.jmb.2016.11.029 · PubMed

Other PDB entries of the same protein (UniProt Q02821 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1WA5 2.0 Å, Structure of the Cse1:Imp-alpha:RanGTP complex
1EE4 2.1 Å, Crystal structure of yeast karyopherin (importin) alpha in a complex with a C-myc nls…
1BK5 2.2 Å, Karyopherin alpha from saccharomyces cerevisiae
5H2X 2.2 Å, Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-172)
4XZR 2.25 Å, Structure of yeast importin a bound to the membrane protein Nuclear Localization Signal…
1EE5 2.4 Å, Yeast karyopherin (importin) alpha in a complex with a nucleoplasmin nls peptide
4PVZ 2.5 Å, Structure of yeast importin a bound to the membrane protein Nuclear Localization Signal…
1UN0 2.6 Å, Crystal Structure of Yeast Karyopherin (Importin) alpha in complex with a Nup2p…
2C1T 2.6 Å, Structure of the Kap60p:Nup2 complex
5T94 2.63 Å, Crystal structure of Kap60 bound to yeast RCC1 (Prp20)
1BK6 2.8 Å, Karyopherin alpha (YEAST) + SV40 T antigen nls

Browse structure collections

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