6X03: Nucleoporin NUP84

Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 and VHH-SAN9. Determined by X-ray diffraction at 7.3 Å resolution. Released 9 Dec 2020.

Method

X-ray diffraction

Resolution

7.3 Å

Organisms

Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Vicugna pacos

Chains

4

Atoms

7,091

Mol. weight

186.71 kDa

Released

9 Dec 2020

Explore 6X03 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X03 contains 84 α-helices and 21 β-strands across 4 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: 45 helices, 0 β-strands

Molecules and chains

>6X03_1 Nucleoporin NUP84 (chains A)
MELSPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDES
NVISSKDWELEARFWHLVELLLVFRNADLDLDEMELHPYNSRGLFEKKLMQDNKQLYQIW
IVMVWLKENTYVMERPKNVPTSKWLNSITSGGLKSCDLDFPLRENTNVLDVKDKEEDHIF
FKYIYELILAGAIDEALEEAKLSDNISICMILCGIQEYLNPVIDTQIANEFNTQQGIKKH
SLWRRTVYSLSQQAGLDPYERAIYSYLSGAIPNQEVLQYSDWESDLHIHLNQILQTEIEN
YLLENNQVGTDELILPLPSHALTVQEVLNRVASRHPSESEHPIRVLMASVILDSLPSVIH
SSVEMLLDVVKGTEASNDIIDKPYLLRIVTHLAICLDIINPGSVEEVDKSKLITTYISLL
KLQGLYENIPIYATFLNESDCLEACSFILSSLEDPQVRKKQIETINFLRLPASNILRRTT
QRVFDETEQEYSPSNEISISFDVNNIDMHLIYGVEWLIEGKLYVDAVHSIIALSRRFLLN
GRVKALEQFMERNNIGEICKNYELEKIADNISKDENEDQFLEEITQYEHLIKGIREYEEW
QKSVSLLSSESNIPTLIEKLQGFSKDTFELIKTFLVDLTSSNFADSADYEILYEIRALYT
PFLLMELHKKLVEAAKLLKIPKFISEALAFTSLVANENDKIYLLFQSSGKLKEYLDLVAR
TATLSN

>6X03_2 Nucleoporin NUP133 (chains B)
MADPGFSLDQESIEHDLKLTSEEIFHSNGKYIPPMLNTLGQHLSVRKEFFQNFLTFVAKN
FNYKISPELKLDLIEKFEILNCCIKFNSIIRQSDVLNDIWEKTLSNYNLTQNEHLTTKTV
VINSPDVFPVIFKQFLNHVVFVLFPSQNQNFKLNVTNLINLCFYDGILEEGEKTIRYELL
ELDPMEVDTSKLPWFINFDYLNCINQCFFDFTFACEEEGSLDSYKEGLLKIVKILYYQFN
QFKIWINTQPVKSVNANDNFININNLYDDNHLDWNHVLCKVNLKEQCIQIAEFYKDLSGL
VQTLQTLDQNDSTTVSLYETFFNEFPKEFSFTLFEYLIKHKKLNDLIFRFPQQHDVLIQF
FQESAPKYGHVAWIQQILDGSYADAMNTLKNITVDDSKKGESLSECELHLNVAKLSSLLV
EKDNLDINTLRKIQYNLDTIDAEKNISNKLKKGEVQICKRFKNGSIREVFNILVEELKST
TVVNLSDLVELYSMLDDEESLFIPLRLLSVDGNLLNFEVKKFLNALVWRRIVLLNASNEG
DKLLQHIVKRVFDEELPKNNDFPLPSVDLLCDKSLLTPEYISETYGRFPIDQNAIREEIY
EEISQVETLNSDNSLEIKLHSTIGSVAKEKNYTINYETNTVEY

>6X03_3 VHH-SAN8 (chains C)
QLQLVETGGGLVQAGGSLRLSCVASGRTFTSYAMGWFRQAPGKEREFVAAISRLASGTDY
ADSVKGRFTISRNNDKNTVYLQMNNLIPEDTAVYYCAALQALRFSLPIAMATMKNGRADS
WGQGTQVTVSS

>6X03_4 VHH-SAN9 (chains D)
QVQLVESGGGSVQAGGSLRLSCAVSGGTLSTLAMGWFRQAPGQEREFVARIGWTNGDTGY
ADSVKGRFTISRDNVKNTVYLQMNNLKPEDTALYYCATRRPYGSTLYPPNTESAHDNWGQ
GTQVTVSS

Primary citation

Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif. Nordeen, S.A., Turman, D.L., Schwartz, T.U. Nat Commun (2020) 11:6060-6060. DOI 10.1038/s41467-020-19885-5 · PubMed

Related structures

Other PDB entries of the same protein (UniProt P52891 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 3IKO 3.2 Å, Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex
• 3JRO 4.0 Å, NUP84-NUP145C-SEC13 edge element of the NPC lattice
• 6X02 6.38 Å, Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8
• 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
• 7N84 11.6 Å, Double nuclear outer ring from the isolated yeast NPC
• 7N9F 37.0 Å, Structure of the in situ yeast NPC
• 8ZZ1 Structure of the Nup84 sub-complex of the Nuclear Pore Complex
• 8ZZA Integrative structure and functional anatomy of a single spoke of a nuclear pore complex
• 8ZZB Integrative structure and functional anatomy of three spokes of a nuclear pore complex
• 8ZZC Integrative structure and functional anatomy of eight spokes of a nuclear pore complex

Browse structure collections

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