5H2V: Karyopherin Kap121p

Crystal structure of the karyopherin Kap121p bound to the SUMO protease Ulp1p. Determined by X-ray diffraction at 2.8 Å resolution. Released 14 Dec 2016.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 2
Atoms: 7,988
Mol. weight: 137.15 kDa
Released: 14 Dec 2016

Explore 5H2V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5H2V contains 71 α-helices and 3 β-strands across 1 chain. 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: 71 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
α-helix	25-33	9
α-helix	34-38	5
α-helix	44-57	14
α-helix	61-77	17
α-helix	91-93	3
α-helix	96-110	15
α-helix	116-127	12
α-helix	135-136	2
α-helix	138-148	11
α-helix	153-165	13
α-helix	169-172	4
α-helix	175-186	12
α-helix	191-207	17
α-helix	210-215	6
α-helix	217-219	3
α-helix	220-232	13
α-helix	236-252	17
α-helix	254-257	4
α-helix	261-273	13
α-helix	279-295	17
α-helix	297-301	5
α-helix	304-318	15
α-helix	329-333	5
α-helix	343-359	17
α-helix	361-375	15
α-helix	381-394	14
α-helix	399-402	4
α-helix	406-413	8
α-helix	414-418	5
α-helix	422-438	17
α-helix	442-457	16
α-helix	465-479	15
α-helix	484-487	4
α-helix	488-490	3
α-helix	491-501	11
α-helix	507-524	18
α-helix	525-531	7
α-helix	532-543	12
α-helix	551-568	18
α-helix	570-573	4
α-helix	577-588	12
α-helix	598-613	16
α-helix	614-620	7
α-helix	621-632	12
β-strand	638-641	4	1
α-helix	645-650	6
β-strand	655-657	3	1
β-strand	664-668	5	1
α-helix	669-689	21
α-helix	690-693	4
α-helix	694-700	7
α-helix	701-705	5
α-helix	706-708	3
α-helix	715-734	20
α-helix	741-757	17
α-helix	764-781	18
α-helix	788-809	22
α-helix	829-848	20
α-helix	853-857	5
α-helix	858-860	3
α-helix	861-869	9
α-helix	873-890	18
α-helix	898-909	12
α-helix	914-930	17
α-helix	936-939	4
α-helix	943-949	7
α-helix	961-977	17
α-helix	987-993	7
α-helix	1002-1016	15
α-helix	1029-1041	13
α-helix	1051-1062	12
α-helix	1071-1073	3
α-helix	1078-1085	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Importin subunit beta-3	A	protein	1078	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32337 (AlphaFold model)
Ubiquitin-like-specific protease 1	B	protein	150	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q02724 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5H2V_1 Importin subunit beta-3 (chains A)
MSALPEEVNRTLLQIVQAFASPDNQIRSVAEKALSEEWITENNIEYLLTFLAEQAAFSQD
TTVAALSAVLFRKLALKAPITHIRKEVLAQIRSSLLKGFLSERADSIRHKLSDAIAECVQ
DDLPAWPELLQALIESLKSGNPNFRESSFRILTTVPYLITAVDINSILPIFQSGFTDASD
NVKIAAVTAFVGYFKQLPKSEWSKLGILLPSLLNSLPRFLDDGKDDALASVFESLIELVE
LAPKLFKDMFDQIIQFTDMVIKNKDLEPPARTTALELLTVFSENAPQMCKSNQNYGQTLV
MVTLIMMTEVSIDDDDAAEWIESDDTDDEEEVTYDHARQALDRVALKLGGEYLAAPLFQY
LQQMITSTEWRERFAAMMALSSAAEGCADVLIGEIPKILDMVIPLINDPHPRVQYGCCNV
LGQISTDFSPFIQRTAHDRILPALISKLTSECTSRVQTHAAAALVNFSEFASKDILEPYL
DSLLTNLLVLLQSNKLYVQEQALTTIAFIAEAAKNKFIKYYDTLMPLLLNVLKVNNKDNS
VLKGKCMECATLIGFAVGKEKFHEHSQELISILVALQNSDIDEDDALRSYLEQSWSRICR
ILGDDFVPLLPIVIPPLLITAKATQDVGLIEEEEAANFQQYPDWDVVQVQGKHIAIHTSV
LDDKVSAMELLQSYATLLRGQFAVYVKEVMEEIALPSLDFYLHDGVRAAGATLIPILLSC
LLAATGTQNEELVLLWHKASSKLIGGLMSEPMPEITQVYHNSLVNGIKVMGDNCLSEDQL
AAFTKGVSANLTDTYERMQDRHGDGDEYNENIDEEEDFTDEDLLDEINKSIAAVLKTTNG
HYLKNLENIWPMINTFLLDNEPILVIFALVVIGDLIQYGGEQTASMKNAFIPKVTECLIS
PDARIRQAASYIIGVCAQYAPSTYADVCIPTLDTLVQIVDFPGSKLEENRSSTENASAAI
AKILYAYNSNIPNVDTYTANWFKTLPTITDKEAASFNYQFLSQLIENNSPIVCAQSNISA
VVDSVIQALNERSLTEREGQTVISSVKKLLGFLPSSDAMAIFNRYPADIMEKVHKWFA

Sequence of entity 2 (B), FASTA

>5H2V_2 Ubiquitin-like-specific protease 1 (chains B)
MSVEVDKHRNTLQYHKKNPYSPLFSPISTYRCYPRVLNNPSESRRSASFSGIYKKRTNTS
RFNYLNDRRVLSMEESMKDGSDRASKAGFIGGIRETLWNSGKYLWHTFVKNEPRNFDGSE
VEASGNSDVESRSSGSRSSDVPYGLRENYS

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 P32337 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3W3W 2.2 Å, Crystal structure of Kap121p bound to Ste12p
4ZJ7 2.4 Å, Crystal structure of the karyopherin Kap121p bound to the extreme C-terminus of the…
3W3U 2.6 Å, Crystal structure of Kap121p mutant R349A/Q350A/D353A/E396A/N430K/D438A/N477A
3W3Z 2.7 Å, Crystal structure of Kap121p bound to RanGTP
3W3Y 2.8 Å, Crystal structure of Kap121p bound to Nup53p
3W3T 2.9 Å, Crystal structure of Kap121p
3W3X 2.9 Å, Crystal structure of Kap121p bound to Pho4p
3W3V 3.2 Å, Crystal structure of Kap121p mutant D353K/E396K/D438K

Browse structure collections

About this viewer

MolViewer shows 5H2V directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.