3IKO: Protein transport protein SEC13

Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex. Determined by X-ray diffraction at 3.2 Å resolution. Released 13 Oct 2009.

Method

X-ray diffraction

Resolution

3.2 Å

Organism

Saccharomyces cerevisiae

Chains

9

Atoms

27,032

Mol. weight

410.88 kDa

Released

13 Oct 2009

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

Secondary structure: helices and β-sheets

3IKO contains 169 α-helices and 132 β-strands across 9 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.

Chains A, D and G: 1 helix, 33 β-strands

Molecules and chains

>3IKO_1 Protein transport protein SEC13 (chains A, D, G)
MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVD
WAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVAS
SDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADN
LVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQ
GPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

>3IKO_2 Nucleoporin NUP145C (chains B, E, H)
MGSSHHHHHHSQDPFSECNDEIDNAKLIMKERRFTASYTFAKFSTGSMLLTKDIVGKSGV
SIKRLPTELQRKFLFDDVYLDKEIEKVTIEARKSNPYPQISESSLLFKDALDYMEKTSSD
YNLWKLSSILFDPVSYPYKTDNDQVKMALLKKERHCRLTSWIVSQIGPEIEEKIRNSSNE
IEQIFLYLLLNDVVRASKLAIESKNGHLSVLISYLGSNDPRIRDLAELQLQKWSTGGCSI
DKNISKIYKLLSGSPFEGLFSLKELESEFSWLCLLNLTLCYGQIDEYSLESLVQSHLDKF
SLPYDDPIGVIFQLYAANENTEKLYKEVRQRTNALDVQFCWYLIQTLRFNGTRVFSKETS
DEATFAFAAQLEFAQLHGHSLFVSCFLNDDKAAEDTIKRLVMREITLLRASTNDHILNRL
KIPSQLIFNAQALKDRYEGNYL

>3IKO_3 Nucleoporin NUP84 (chains C, F, I)
MELSPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDES
NVISSKDWELEARFWHLVELLLVFRNADLDLDEMELHPYNSRGLFEKKLMQDNKQLYQIW
IVMVWLKENTYVMERPKNVPTSKWLNSITSGGLKSCDLDFPLRENTNVLDVKDKEEDHIF
FKYIYELILAGAIDEALEEAKLSDNISICMILCGIQEYLNPVIDTQIANEFNTQQGIKKH
SLWRRTVYSLSQQAGLDPYERAIYSYLSGAIPNQEVLQYSDWESDLHIHLNQILQTEIEN
YLLENNQVGTDELILPLPSHALTVQEVLNRVASRHPSESEHPIRVLMASVILDSLPSVIH
SSVEMLLDVVKGTEASNDIIDKPYLLRIVTHLAICLDIINPGSVEEVDKSKLITTYISLL
KLQGLYENIPIYATFLNESDCLEACSFILSSLEDPQVRKK

Primary citation

Structure of a trimeric nucleoporin complex reveals alternate oligomerization states. Nagy, V., Hsia, K.C., Debler, E.W. et al. Proc Natl Acad Sci U S A (2009) 106:17693-17698. DOI 10.1073/pnas.0909373106 · PubMed

Related structures

Other PDB entries of the same protein (UniProt Q04491 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 2PM7 2.35 Å, Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat,…
• 2PM6 2.45 Å, Crystal Structure of yeast Sec13/31 edge element of the COPII vesicular coat, native…
• 3JRP 2.6 Å, SEC13 with NUP145C (AA109-179) insertion blade
• 3MZK 2.69 Å, Sec13/Sec16 complex, S.cerevisiae
• 3MZL 2.8 Å, Sec13/Sec31 edge element, loop deletion mutant
• 8ADL 2.95 Å, Cryo-EM structure of the SEA complex
• 9H5K 3.2 Å, Cryo-EM structure of the SEAC-EGOC supercomplex
• 2PM9 3.3 Å, Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat
• 3JRO 4.0 Å, NUP84-NUP145C-SEC13 edge element of the NPC lattice
• 4XMM 7.38 Å, Structure of the yeast coat nucleoporin complex, space group C2
• 4XMN 7.6 Å, Structure of the yeast coat nucleoporin complex, space group P212121
• 8TIE 8.1 Å, Double nuclear outer ring of Nup84-complexes from the yeast NPC

Browse structure collections

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