6x06

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Nup120 (aa1-757) from S. cerevisiae bound by VHH-SAN11

Structural highlights

6x06 is a 2 chain structure with sequence from Saccharomyces cerevisiae S288C and Vicugna pacos. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 4.27Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NU120_YEAST Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. NUP120 is involved in nuclear poly(A)+ RNA and pre-ribosome export, in GSP1 nuclear import, in NPC assembly and distribution, as well as in nuclear envelope organization.[1] [2] [3] [4] [5]

Publication Abstract from PubMed

Nuclear pore complexes (NPCs) are the main conduits for molecular exchange across the nuclear envelope. The NPC is a modular assembly of ~500 individual proteins, called nucleoporins or nups. Most scaffolding nups are organized in two multimeric subcomplexes, the Nup84 or Y complex and the Nic96 or inner ring complex. Working in S. cerevisiae, and to study the assembly of these two essential subcomplexes, we here develop a set of twelve nanobodies that recognize seven constituent nucleoporins of the Y and Nic96 complexes. These nanobodies all bind specifically and with high affinity. We present structures of several nup-nanobody complexes, revealing their binding sites. Additionally, constitutive expression of the nanobody suite in S. cerevisiae detect accessible and obstructed surfaces of the Y complex and Nic96 within the NPC. Overall, this suite of nanobodies provides a unique and versatile toolkit for the study of the NPC.

A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure.,Nordeen SA, Andersen KR, Knockenhauer KE, Ingram JR, Ploegh HL, Schwartz TU Nat Commun. 2020 Dec 2;11(1):6179. doi: 10.1038/s41467-020-19884-6. PMID:33268786[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
1 reviews cite this structure
V<sub>H</sub>H Structural Modelling Approaches: A Critical Review.
Vishwakarma et al. (2022)
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7 other articles
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See Also

References

  1. ↑ Heath CV, Copeland CS, Amberg DC, Del Priore V, Snyder M, Cole CN. Nuclear pore complex clustering and nuclear accumulation of poly(A)+ RNA associated with mutation of the Saccharomyces cerevisiae RAT2/NUP120 gene. J Cell Biol. 1995 Dec;131(6 Pt 2):1677-97. PMID:8557737
  2. ↑ Siniossoglou S, Wimmer C, Rieger M, Doye V, Tekotte H, Weise C, Emig S, Segref A, Hurt EC. A novel complex of nucleoporins, which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores. Cell. 1996 Jan 26;84(2):265-75. PMID:8565072
  3. ↑ Stage-Zimmermann T, Schmidt U, Silver PA. Factors affecting nuclear export of the 60S ribosomal subunit in vivo. Mol Biol Cell. 2000 Nov;11(11):3777-89. PMID:11071906
  4. ↑ Lutzmann M, Kunze R, Buerer A, Aebi U, Hurt E. Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins. EMBO J. 2002 Feb 1;21(3):387-97. PMID:11823431 doi:10.1093/emboj/21.3.387
  5. ↑ Gao H, Sumanaweera N, Bailer SM, Stochaj U. Nuclear accumulation of the small GTPase Gsp1p depends on nucleoporins Nup133p, Rat2p/Nup120p, Nup85p, Nic96p, and the acetyl-CoA carboxylase Acc1p. J Biol Chem. 2003 Jul 11;278(28):25331-40. Epub 2003 May 1. PMID:12730220 doi:http://dx.doi.org/10.1074/jbc.M301607200
  6. ↑ Nordeen SA, Andersen KR, Knockenhauer KE, Ingram JR, Ploegh HL, Schwartz TU. A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure. Nat Commun. 2020 Dec 2;11(1):6179. PMID:33268786 doi:10.1038/s41467-020-19884-6

Contents


PDB ID 6x06

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OCA

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