9D45: Yeast Exportin Msn5

Cryo-EM structure of yeast Exportin Msn5 bound to cargo Pho4 and RanGTP. Determined by electron microscopy at 3.1 Å resolution. Released 19 Mar 2025.

Method
Electron microscopy
Resolution
3.1 Å
Organism
Saccharomyces cerevisiae
Chains
3
Atoms
11,123
Mol. weight
187.4 kDa
Ligands
MG, GTP
Released
19 Mar 2025

Explore 9D45 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D45 contains 85 α-helices and 11 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: 79 helices, 4 β-strands

ElementResiduesLengthSheet
α-helix6-1712
α-helix23-3715
α-helix42-5211
α-helix57-7216
α-helix80-9516
α-helix103-12018
α-helix123-1264
α-helix132-1376
α-helix142-1498
α-helix154-16815
α-helix169-1735
α-helix177-1815
α-helix183-19412
α-helix197-2037
α-helix208-2136
α-helix221-23414
α-helix237-24812
α-helix256-2616
α-helix264-2729
α-helix277-29216
α-helix298-30912
α-helix312-32211
α-helix335-34612
α-helix348-3547
α-helix361-37313
α-helix378-3814
α-helix385-3939
α-helix398-4025
α-helix406-41510
α-helix420-4223
α-helix428-4358
α-helix439-46325
α-helix465-48117
α-helix483-4897
α-helix499-52426
α-helix531-55020
α-helix557-57418
α-helix575-5784
α-helix579-58911
α-helix599-6013
α-helix604-62623
α-helix628-6325
α-helix635-64511
α-helix646-6483
α-helix651-66717
α-helix673-68513
α-helix686-6894
α-helix691-6966
α-helix700-7078
α-helix709-71810
β-strand73111
α-helix7321
α-helix734-75017
α-helix753-76412
α-helix770-78415
α-helix788-80013
α-helix804-8063
α-helix812-8143
α-helix815-8228
α-helix836-84712
β-strand84911
α-helix851-87727
α-helix880-8845
α-helix888-8969
β-strand89912
β-strand90612
α-helix912-9187
α-helix919-9235
α-helix924-9285
α-helix935-96733
α-helix974-100128
α-helix1018-102811
α-helix1031-104616
α-helix1050-106718
α-helix1072-10776
α-helix1078-10825
α-helix1083-10853
α-helix1086-10916
α-helix1094-10963
α-helix1097-111721
α-helix1119-112911
α-helix1134-114310
α-helix1147-116317
Chain B: 5 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand12-1983
α-helix25-339
β-strand47-56103
β-strand59-68103
α-helix79-824
β-strand88-9363
α-helix97-11115
β-strand119-12463
α-helix140-1434
β-strand147-15043
α-helix161-17111
β-strand17813
Chain C: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix113-1153

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Protein MSN5Aprotein1230Saccharomyces cerevisiaeP52918 (AlphaFold model)
GTP-binding nuclear protein GSP1/CNR1Bprotein186Saccharomyces cerevisiaeP32835 (AlphaFold model)
Phosphate system positive regulatory protein PHO4Cprotein202Saccharomyces cerevisiaeP07270 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9D45_1 Protein MSN5 (chains A)
MDSTGASQIVSALDVIYSPKSNNSQRQEAQKFLDEVKLCSESPFWGYEIALQNPTNSILK
YFGLGLLDHAVKKNWNDYDEGKRVALRKWVMELNFGVQDYDTRYIKEKLATLWVEVAKRT
WGEALKQTNPTEEQLLTSWVDMDNNLFELWNINQSSRELALIIFRILFEDVFLLDDLIVL
KRMTVIQPLCVMIVCPIEVFAIKYKFSDKWTKFKANEEGWFSVWIPELNNALQQNNSEYI
IRLLETLKTCLNWPLTEVIVRNDVLSSLLTCLSSNIPRAQSMALDSIHILLTRPYSNESH
YQMTIDRVFDNMDLLDSVYESLLFDPTDDIDETKYPIIKKFVDMISCLYVCVPKIKETNG
QIQKYFKLVLKTTYNPSLIVSGLTLDLWCTCLRNDEYLPKLEKYVIPDLLQFAADALVYY
EQIDGHISKKFAEIDFQSKSEFQTFCSTYRKRIRDIIRLISCVELDLTYDWLNNRLNNYF
SSPFGQQVLSSTFLDHKLEPYLGALSQYMIVECFINGCIRWKIWYPTGDDYDEKLDSILQ
KLEILSNQLIALNLREPLLLKKQIQNFALFLTMLKDNVLFTLLEKIITSATMDYPEINLE
ERGAESDAVRDLRYACGIELNRMALLMPESLKKIYPDLESVIARIMPNLSYHEKISFKSF
LLIIVLKSSLDMKEERFAAIVDPELLAWSDKTTVVGLSDLHWFMERLGIVQIAEYFQRRD
IDENSDLLSIPIDDEGKELKSELTKRWQSLFPVRATRMFIHYSMQSIKTDEEFKMLQDLW
RPRIVPILPYITRLLYQLQSYHDPDNWKGLPTVVQSFVKYSTIERFWEAGASNKSKDEFI
DEHMKAMQTLRDFADSVGHIIRYTREYTLLVLSAISSLGSVFYLLDESPDLLLNSIAIFK
PGSNEISPGVSTHGWKHIMNIAIRPILKGCPKDCLGKFMPAFLPKLFEILDLLLCQKWSS
HMNDMDMNPVPTDDDQMTEEILEENLLRQLTTVVVRIVIDCVGQGNANPNSAKSRLNNHQ
MEMRKIIFNDLNTLAPFLKLLNHLISFKDTKCSFNSILVMKCCLTSVLNQNNTVDEYFTF
EVMKNLLLNVLCNSAFKDSFHEALYAFTVIFLTLCKEYPSARAFLFEISNGYNIDELYRN
LRSVDEYKTQRALMIDFIDWVKSTSGKEDGNVDHAGDERKRQEKREAILKKANERLIKKN
KENGDMLDDPNIEDGAVGNLFDDNENLYFQ
Sequence of entity 2 (B), FASTA
>9D45_2 GTP-binding nuclear protein GSP1/CNR1 (chains B)
MASAPAANGEVPTFKLVLVGDGGTGKTTFVKRHLTGEFEKKYIATIGVEVHPLSFYTNFG
EIKFDVWDTAGLEKFGGLRDGYYINAQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPI
VLCGNKVDVKERKVKAKTITFHRKKNLQYYDISAKSNYNFEKPFLWLARKLAGNPQLEFV
ENLYFQ
Sequence of entity 3 (C), FASTA
>9D45_3 Phosphate system positive regulatory protein PHO4 (chains C)
GSMGRTTSEGIHGFVDDLEPKSSILDKVGDFITVNTKRHDGREDFNEQNDELNSQENHNS
SENGNENENEQDSLALDDLDRAFELVEGMDMDWMMPSHAHHSPATTATIKPRLLYSPLIH
TQSAVPVTISPNLVATATSTTSANKVTKNKSNSSPYLNKRRGKPGPDSATSLFELPDSVI
PTPKPKPKPKQYPKVILPSNST

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg1
GTPGuanosine-5'-triphosphateC10 H16 N5 O14 P31

Primary citation

Phosphate-dependent nuclear export via a non-classical NES class recognized by exportin Msn5. Fung, H.Y.J., Mittal, S.R., Niesman, A.B. et al. Nat Commun (2025) 16:2580-2580. DOI 10.1038/s41467-025-57752-3 · PubMed

Other PDB entries of the same protein (UniProt P52918 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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