3W3Z: Kap121p

Crystal structure of Kap121p bound to RanGTP. Determined by X-ray diffraction at 2.7 Å resolution. Released 10 Apr 2013.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Saccharomyces cerevisiae, Canis lupus familiaris
Chains: 2
Atoms: 9,146
Mol. weight: 143.06 kDa
Ligands: MG, GTP
Released: 10 Apr 2013

Explore 3W3Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3W3Z contains 80 α-helices and 11 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: 72 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
α-helix	24-32	9
α-helix	33-37	5
α-helix	44-57	14
α-helix	61-76	16
α-helix	96-111	16
α-helix	116-127	12
α-helix	135-136	2
α-helix	138-149	12
α-helix	153-165	13
α-helix	167-170	4
α-helix	180-185	6
α-helix	191-207	17
α-helix	210-212	3
α-helix	214-217	4
α-helix	220-226	7
α-helix	228-232	5
α-helix	236-250	15
α-helix	254-260	7
α-helix	261-273	13
α-helix	279-295	17
α-helix	297-301	5
α-helix	304-318	15
α-helix	329-332	4
α-helix	343-359	17
α-helix	361-376	16
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	442-458	17
α-helix	465-480	16
α-helix	484-487	4
α-helix	488-490	3
α-helix	491-502	12
α-helix	507-520	14
α-helix	524-526	3
α-helix	528-543	16
α-helix	551-567	17
α-helix	569-588	20
α-helix	597-613	17
α-helix	614-620	7
α-helix	621-631	11
α-helix	634-636	3
β-strand	638-641	4	1
α-helix	642	1
α-helix	645-648	4
α-helix	649-651	3
β-strand	655-659	5	1
β-strand	664-668	5	1
α-helix	669-689	21
α-helix	690-693	4
α-helix	694-699	6
α-helix	700-705	6
α-helix	706-708	3
α-helix	715-735	21
α-helix	742-760	19
α-helix	764-781	18
α-helix	788-809	22
α-helix	830-849	20
α-helix	854-859	6
α-helix	861-868	8
α-helix	874-888	15
α-helix	895-909	15
α-helix	914-930	17
α-helix	936-949	14
α-helix	961-977	17
α-helix	987-993	7
α-helix	1002-1015	14
α-helix	1030-1041	12
α-helix	1053-1062	10
α-helix	1066-1071	6
α-helix	1072-1075	4
α-helix	1078-1085	8

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-16	8	2
α-helix	23-32	10
α-helix	34-36	3
β-strand	45-55	11	2
β-strand	57-66	10	2
α-helix	70-73	4
α-helix	76-78	3
β-strand	85-91	7	2
α-helix	95-99	5
α-helix	101-111	11
β-strand	117-122	6	2
α-helix	138-142	5
β-strand	145-148	4	2
β-strand	150	1	3
β-strand	155	1	3
α-helix	159-169	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Importin subunit beta-3	A	protein	1089	Saccharomyces cerevisiae	P32337 (AlphaFold model)
GTP-binding nuclear protein Ran	B	protein	176	Canis lupus familiaris	P62825 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3W3Z_1 Importin subunit beta-3 (chains A)
MSALPEEVNRTLLQIVQAFASPDNQIRSVAEKALSEEWITENNIEYLLTFLAEQAAFSQD
TTVAALSAVLFRKLALKAPPSSKLMIMSKNITHIRKEVLAQIRSSLLKGFLSERADSIRH
KLSDAIAECVQDDLPAWPELLQALIESLKSGNPNFRESSFRILTTVPYLITAVDINSILP
IFQSGFTDASDNVKIAAVTAFVGYFKQLPKSEWSKLGILLPSLLNSLPRFLDDGKDDALA
SVFESLIELVELAPKLFKDMFDQIIQFTDMVIKNKDLEPPARTTALELLTVFSENAPQMC
KSNQNYGQTLVMVTLIMMTEVSIDDDDAAEWIESDDTDDEEEVTYDHARQALDRVALKLG
GEYLAAPLFQYLQQMITSTEWRERFAAMMALSSAAEGCADVLIGEIPKILDMVIPLINDP
HPRVQYGCCNVLGQISTDFSPFIQRTAHDRILPALISKLTSECTSRVQTHAAAALVNFSE
FASKDILEPYLDSLLTNLLVLLQSNKLYVQEQALTTIAFIAEAAKNKFIKYYDTLMPLLL
NVLKVNNKDNSVLKGKCMECATLIGFAVGKEKFHEHSQELISILVALQNSDIDEDDALRS
YLEQSWSRICRILGDDFVPLLPIVIPPLLITAKATQDVGLIEEEEAANFQQYPDWDVVQV
QGKHIAIHTSVLDDKVSAMELLQSYATLLRGQFAVYVKEVMEEIALPSLDFYLHDGVRAA
GATLIPILLSCLLAATGTQNEELVLLWHKASSKLIGGLMSEPMPEITQVYHNSLVNGIKV
MGDNCLSEDQLAAFTKGVSANLTDTYERMQDRHGDGDEYNENIDEEEDFTDEDLLDEINK
SIAAVLKTTNGHYLKNLENIWPMINTFLLDNEPILVIFALVVIGDLIQYGGEQTASMKNA
FIPKVTECLISPDARIRQAASYIIGVCAQYAPSTYADVCIPTLDTLVQIVDFPGSKLEEN
RSSTENASAAIAKILYAYNSNIPNVDTYTANWFKTLPTITDKEAASFNYQFLSQLIENNS
PIVCAQSNISAVVDSVIQALNERSLTEREGQTVISSVKKLLGFLPSSDAMAIFNRYPADI
MEKVHKWFA

Sequence of entity 2 (B), FASTA

>3W3Z_2 GTP-binding nuclear protein Ran (chains B)
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

Structural basis for cell-cycle-dependent nuclear import mediated by the karyopherin Kap121p. Kobayashi, J., Matsuura, Y. J Mol Biol (2013) 425:1852-1868. DOI 10.1016/j.jmb.2013.02.035 · 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
3W3Y 2.8 Å, Crystal structure of Kap121p bound to Nup53p
5H2V 2.8 Å, Crystal structure of the karyopherin Kap121p bound to the SUMO protease Ulp1p
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 3W3Z 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.