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1.I.1.1.1
Nuclear Pore Complex (NPC) (Tran and Wente, 2006).  The structure of the NPC core (400kD) has been determined at 7.4 Å resolution revealing a curved Y-shaped architecture with the coat nucleoporin interactions forming the central ""triskeleton"".  32 copies of the coat neucloporin complex (CNC) structure dock into the cryoelectron tomographic reconstruction of the assembled human NPC, thus accounting for ~16 MDa of it's mass (Stuwe et al. 2015).  Import of integral membrane proteins (mono- and polytopic) into the the inner nuclear membrane occurs by an active, transport factor-dependent process (Laba et al. 2015). Ndc1 and Pom52 are partially redundant NPC components that are essential for proper assembly of the NPC. The absence of Ndc1p and Pom152p results in aberrant pores that have enlarged diameters and lack proteinaceous material, leading to increased diffusion between the cytoplasm and the nucleus (Madrid et al. 2006). Pom152 is a transmembrane protein within the nuclear pore complex (NPC) of fungi that is important for NPC assembly and structure. Pom152 is comprised of a short amino-terminal region that remains on the cytosolic side of the nuclear envelope (NE) and interacts with NPC proteins, a transmembrane domain, and a large, glycosylated carboxy-terminal domain within the NE lumen. Here we show that the N-terminal 200 amino acids of Pom152 that include only the amino-terminal and transmembrane regions are sufficient for localization to the NPC (Brown et al. 2021). Atg39 selectively captures the inner nuclear membrane into lumenal vesicles for delivery to the autophagosome (Chandra et al. 2021). The inner nuclear membrane (INM) changes its protein composition during gametogenesis, sheding light on mechanisms used to shape the INM proteome of spores (Shelton et al. 2021). Several nucleoporins with FG-repeats (phenylalanine-glycine repeats) (barrier nucleoporins) possess potential amyloidogenic properties (Danilov et al. 2023).  A multiscale structure of the yeast nuclear pore complex has been described, and its implications have been discussed (Akey et al. 2023).  NPCs direct the nucleocytoplasmic transport of macromolecules, and Akey et al. 2023 provided a composite multiscale structure of the yeast NPC, based on improved 3D density maps from cryoEM and AlphaFold2 models. Key features of the inner and outer rings were integrated into a comprehensive model. The authors resolved flexible connectors that tie together the core scaffold, along with equatorial transmembrane complexes and a lumenal ring that anchor this channel within the pore membrane. The organization of the nuclear double outer ring revealed an architecture that may be shared with ancestral NPCs. Additional connections between the core scaffold and the central transporter suggest that under certain conditions, a degree of local organization is present at the periphery of the transport machinery. These connectors may couple conformational changes in the scaffold to the central transporter to modulate transport. Collectively, this analysis provides insights into assembly, transport, and NPC evolution (Akey et al. 2023).

Accession Number:P39705
Protein Name:Nucleoporin NUP60
Length:539
Molecular Weight:59039.00
Species:Saccharomyces cerevisiae (Baker's yeast) [4932]
Location1 / Topology2 / Orientation3: Nucleus1 / Peripheral membrane protein2 / Nucleoplasmic side3
Substrate

Cross database links:

DIP: DIP-5821N DIP-5821N DIP-5821N DIP-5821N
RefSeq: NP_009401.1   
Entrez Gene ID: 851263   
KEGG: sce:YAR002W    sce:YAR002W    sce:YAR002W    sce:YAR002W   

Gene Ontology

GO:0031965 C:nuclear membrane
GO:0005643 C:nuclear pore
GO:0005515 F:protein binding
GO:0017056 F:structural constituent of nuclear pore
GO:0051028 P:mRNA transport
GO:0000059 P:protein import into nucleus, docking
GO:0055085 P:transmembrane transport
GO:0005543 F:phospholipid binding
GO:0006302 P:double-strand break repair
GO:0008298 P:intracellular mRNA localization
GO:0031990 P:mRNA export from nucleus in response to heat stress
GO:0006607 P:NLS-bearing substrate import into nucleus
GO:0016973 P:poly(A)+ mRNA export from nucleus
GO:0000973 P:posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery
GO:0006611 P:protein export from nucleus
GO:0060188 P:regulation of protein desumoylation
GO:0034398 P:telomere tethering at nuclear periphery

References (64)

[1] “Sequencing of chromosome I of Saccharomyces cerevisiae: analysis of the 42 kbp SPO7-CENI-CDC15 region.”  Clark M.W.et.al.   7941740
[2] “The nucleotide sequence of chromosome I from Saccharomyces cerevisiae.”  Bussey H.et.al.   7731988
[3] “Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.”  Hu Y.et.al.   17322287
[4] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[5] “Proteomic analysis of nucleoporin interacting proteins.”  Allen N.P.et.al.   11387327
[6] “The nucleoporin Nup60p functions as a Gsp1p-GTP-sensitive tether for Nup2p at the nuclear pore complex.”  Denning D.P.et.al.   11535617
[7] “Global analysis of protein expression in yeast.”  Ghaemmaghami S.et.al.   14562106
[8] “Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.”  Denning D.P.et.al.   12604785
[9] “Minimal nuclear pore complexes define FG repeat domains essential for transport.”  Strawn L.A.et.al.   15039779
[10] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[11] “Targets of the cyclin-dependent kinase Cdk1.”  Ubersax J.A.et.al.   14574415
[12] “Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.”  Gruhler A.et.al.   15665377
[13] “Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.”  Li X.et.al.   17330950
[14] “Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.”  Chi A.et.al.   17287358
[15] “Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.”  Smolka M.B.et.al.   17563356
[16] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[17] “Sequencing of chromosome I of Saccharomyces cerevisiae: analysis of the 42 kbp SPO7-CENI-CDC15 region.”  Clark M.W.et.al.   7941740
[18] “The nucleotide sequence of chromosome I from Saccharomyces cerevisiae.”  Bussey H.et.al.   7731988
[19] “Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.”  Hu Y.et.al.   17322287
[20] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[21] “Proteomic analysis of nucleoporin interacting proteins.”  Allen N.P.et.al.   11387327
[22] “The nucleoporin Nup60p functions as a Gsp1p-GTP-sensitive tether for Nup2p at the nuclear pore complex.”  Denning D.P.et.al.   11535617
[23] “Global analysis of protein expression in yeast.”  Ghaemmaghami S.et.al.   14562106
[24] “Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.”  Denning D.P.et.al.   12604785
[25] “Minimal nuclear pore complexes define FG repeat domains essential for transport.”  Strawn L.A.et.al.   15039779
[26] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[27] “Targets of the cyclin-dependent kinase Cdk1.”  Ubersax J.A.et.al.   14574415
[28] “Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.”  Gruhler A.et.al.   15665377
[29] “Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.”  Li X.et.al.   17330950
[30] “Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.”  Chi A.et.al.   17287358
[31] “Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.”  Smolka M.B.et.al.   17563356
[32] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[33] “Sequencing of chromosome I of Saccharomyces cerevisiae: analysis of the 42 kbp SPO7-CENI-CDC15 region.”  Clark M.W.et.al.   7941740
[34] “The nucleotide sequence of chromosome I from Saccharomyces cerevisiae.”  Bussey H.et.al.   7731988
[35] “Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.”  Hu Y.et.al.   17322287
[36] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[37] “Proteomic analysis of nucleoporin interacting proteins.”  Allen N.P.et.al.   11387327
[38] “The nucleoporin Nup60p functions as a Gsp1p-GTP-sensitive tether for Nup2p at the nuclear pore complex.”  Denning D.P.et.al.   11535617
[39] “Global analysis of protein expression in yeast.”  Ghaemmaghami S.et.al.   14562106
[40] “Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.”  Denning D.P.et.al.   12604785
[41] “Minimal nuclear pore complexes define FG repeat domains essential for transport.”  Strawn L.A.et.al.   15039779
[42] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[43] “Targets of the cyclin-dependent kinase Cdk1.”  Ubersax J.A.et.al.   14574415
[44] “Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.”  Gruhler A.et.al.   15665377
[45] “Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.”  Li X.et.al.   17330950
[46] “Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.”  Chi A.et.al.   17287358
[47] “Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.”  Smolka M.B.et.al.   17563356
[48] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[49] “Sequencing of chromosome I of Saccharomyces cerevisiae: analysis of the 42 kbp SPO7-CENI-CDC15 region.”  Clark M.W.et.al.   7941740
[50] “The nucleotide sequence of chromosome I from Saccharomyces cerevisiae.”  Bussey H.et.al.   7731988
[51] “Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.”  Hu Y.et.al.   17322287
[52] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[53] “Proteomic analysis of nucleoporin interacting proteins.”  Allen N.P.et.al.   11387327
[54] “The nucleoporin Nup60p functions as a Gsp1p-GTP-sensitive tether for Nup2p at the nuclear pore complex.”  Denning D.P.et.al.   11535617
[55] “Global analysis of protein expression in yeast.”  Ghaemmaghami S.et.al.   14562106
[56] “Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.”  Denning D.P.et.al.   12604785
[57] “Minimal nuclear pore complexes define FG repeat domains essential for transport.”  Strawn L.A.et.al.   15039779
[58] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[59] “Targets of the cyclin-dependent kinase Cdk1.”  Ubersax J.A.et.al.   14574415
[60] “Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.”  Gruhler A.et.al.   15665377
[61] “Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.”  Li X.et.al.   17330950
[62] “Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.”  Chi A.et.al.   17287358
[63] “Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.”  Smolka M.B.et.al.   17563356
[64] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956

External Searches:

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Predict TMSs (Predict number of transmembrane segments)
Window Size: Angle:  
FASTA formatted sequence
1:	MHRKSLRRAS ATVPSAPYRK QIISNAHNKP SLFSKIKTFF TQKDSARVSP RNNVANKQPR 
61:	NESFNRRISS MPGGYFHSEI SPDSTVNRSV VVSAVGEARN DIENKEEEYD ETHETNISNA 
121:	KLANFFSKKG NEPLSEIEIE GVMSLLQKSS KSMITSEGEQ KSAEGNNIDQ SLILKESGST 
181:	PISISNAPTF NPKYDTSNAS MNTTLGSIGS RKYSFNYSSL PSPYKTTVYR YSAAKKIPDT 
241:	YTANTSAQSI ASAKSVRSGV SKSAPSKKIS NTAAALVSLL DENDSKKNNA ASELANPYSS 
301:	YVSQIRKHKR VSPNAAPRQE ISEEETTVKP LFQNVPEQGE EPMKQLNATK ISPSAPSKDS 
361:	FTKYKPARSS SLRSNVVVAE TSPEKKDGGD KPPSSAFNFS FNTSRNVEPT ENAYKSENAP 
421:	SASSKEFNFT NLQAKPLVGK PKTELTKGDS TPVQPDLSVT PQKSSSKGFV FNSVQKKSRS 
481:	NLSQENDNEG KHISASIDND FSEEKAEEFD FNVPVVSKQL GNGLVDENKV EAFKSLYTF