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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:P49686
Protein Name:Nucleoporin NUP42
Length:430
Molecular Weight:42778.00
Species:Saccharomyces cerevisiae (Baker's yeast) [4932]
Location1 / Topology2 / Orientation3: Nucleus1 / Peripheral membrane protein2 / Cytoplasmic side3
Substrate

Cross database links:

DIP: DIP-2313N DIP-2313N DIP-2313N DIP-2313N
RefSeq: NP_010478.1   
Entrez Gene ID: 851774   
KEGG: sce:YDR192C    sce:YDR192C    sce:YDR192C    sce:YDR192C   

Gene Ontology

GO:0031965 C:nuclear membrane
GO:0005643 C:nuclear pore
GO:0042802 F:identical protein binding
GO:0005198 F:structural molecule activity
GO:0006406 P:mRNA export from nucleus
GO:0006609 P:mRNA-binding (hnRNP) protein import into nu...
GO:0006607 P:NLS-bearing substrate import into nucleus
GO:0006999 P:nuclear pore organization
GO:0006611 P:protein export from nucleus
GO:0006610 P:ribosomal protein import into nucleus
GO:0006407 P:rRNA export from nucleus
GO:0006408 P:snRNA export from nucleus
GO:0006608 P:snRNP protein import into nucleus
GO:0055085 P:transmembrane transport
GO:0006409 P:tRNA export from nucleus
GO:0031990 P:mRNA export from nucleus in response to heat stress
GO:0016973 P:poly(A)+ mRNA export from nucleus
GO:0000973 P:posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery
GO:0015031 P:protein transport
GO:0005515 F:protein binding

References (56)

[1] “Identification of a novel nuclear pore-associated protein as a functional target of the HIV-1 Rev protein in yeast.”  Stutz F.et.al.   7634338
[2] “The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.”  Jacq C.et.al.   9169867
[3] “Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.”  Hu Y.et.al.   17322287
[4] “The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr255p.”  Strahm Y.et.al.   10610322
[5] “Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells.”  Hodge C.A.et.al.   10523319
[6] “Binding of the Mex67p/Mtr2p heterodimer to FXFG, GLFG, and FG repeat nucleoporins is essential for nuclear mRNA export.”  Straesser K.et.al.   10952996
[7] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[8] “Nuclear export of heat shock and non-heat-shock mRNA occurs via similar pathways.”  Vainberg I.E.et.al.   10805742
[9] “Proteomic analysis of nucleoporin interacting proteins.”  Allen N.P.et.al.   11387327
[10] “A gradient of affinity for the karyopherin Kap95p along the yeast nuclear pore complex.”  Pyhtila B.et.al.   12917401
[11] “Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.”  Denning D.P.et.al.   12604785
[12] “Minimal nuclear pore complexes define FG repeat domains essential for transport.”  Strawn L.A.et.al.   15039779
[13] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[14] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[15] “Identification of a novel nuclear pore-associated protein as a functional target of the HIV-1 Rev protein in yeast.”  Stutz F.et.al.   7634338
[16] “The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.”  Jacq C.et.al.   9169867
[17] “Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.”  Hu Y.et.al.   17322287
[18] “The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr255p.”  Strahm Y.et.al.   10610322
[19] “Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells.”  Hodge C.A.et.al.   10523319
[20] “Binding of the Mex67p/Mtr2p heterodimer to FXFG, GLFG, and FG repeat nucleoporins is essential for nuclear mRNA export.”  Straesser K.et.al.   10952996
[21] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[22] “Nuclear export of heat shock and non-heat-shock mRNA occurs via similar pathways.”  Vainberg I.E.et.al.   10805742
[23] “Proteomic analysis of nucleoporin interacting proteins.”  Allen N.P.et.al.   11387327
[24] “A gradient of affinity for the karyopherin Kap95p along the yeast nuclear pore complex.”  Pyhtila B.et.al.   12917401
[25] “Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.”  Denning D.P.et.al.   12604785
[26] “Minimal nuclear pore complexes define FG repeat domains essential for transport.”  Strawn L.A.et.al.   15039779
[27] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[28] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[29] “Identification of a novel nuclear pore-associated protein as a functional target of the HIV-1 Rev protein in yeast.”  Stutz F.et.al.   7634338
[30] “The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.”  Jacq C.et.al.   9169867
[31] “Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.”  Hu Y.et.al.   17322287
[32] “The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr255p.”  Strahm Y.et.al.   10610322
[33] “Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells.”  Hodge C.A.et.al.   10523319
[34] “Binding of the Mex67p/Mtr2p heterodimer to FXFG, GLFG, and FG repeat nucleoporins is essential for nuclear mRNA export.”  Straesser K.et.al.   10952996
[35] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[36] “Nuclear export of heat shock and non-heat-shock mRNA occurs via similar pathways.”  Vainberg I.E.et.al.   10805742
[37] “Proteomic analysis of nucleoporin interacting proteins.”  Allen N.P.et.al.   11387327
[38] “A gradient of affinity for the karyopherin Kap95p along the yeast nuclear pore complex.”  Pyhtila B.et.al.   12917401
[39] “Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.”  Denning D.P.et.al.   12604785
[40] “Minimal nuclear pore complexes define FG repeat domains essential for transport.”  Strawn L.A.et.al.   15039779
[41] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[42] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[43] “Identification of a novel nuclear pore-associated protein as a functional target of the HIV-1 Rev protein in yeast.”  Stutz F.et.al.   7634338
[44] “The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.”  Jacq C.et.al.   9169867
[45] “Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.”  Hu Y.et.al.   17322287
[46] “The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr255p.”  Strahm Y.et.al.   10610322
[47] “Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells.”  Hodge C.A.et.al.   10523319
[48] “Binding of the Mex67p/Mtr2p heterodimer to FXFG, GLFG, and FG repeat nucleoporins is essential for nuclear mRNA export.”  Straesser K.et.al.   10952996
[49] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[50] “Nuclear export of heat shock and non-heat-shock mRNA occurs via similar pathways.”  Vainberg I.E.et.al.   10805742
[51] “Proteomic analysis of nucleoporin interacting proteins.”  Allen N.P.et.al.   11387327
[52] “A gradient of affinity for the karyopherin Kap95p along the yeast nuclear pore complex.”  Pyhtila B.et.al.   12917401
[53] “Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.”  Denning D.P.et.al.   12604785
[54] “Minimal nuclear pore complexes define FG repeat domains essential for transport.”  Strawn L.A.et.al.   15039779
[55] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[56] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
Structure:
6B4E     

External Searches:

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Predict TMSs (Predict number of transmembrane segments)
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FASTA formatted sequence
1:	MSAFGNPFTS GAKPNLSNTS GINPFTNNAA STNNMGGSAF GRPSFGTANT MTGGTTTSAF 
61:	GMPQFGTNTG NTGNTSISAF GNTSNAAKPS AFGAPAFGSS APINVNPPST TSAFGAPSFG 
121:	STGFGAMAAT SNPFGKSPGS MGSAFGQPAF GANKTAIPSS SVSNSNNSAF GAASNTPLTT 
181:	TSPFGSLQQN ASQNASSTSS AFGKPTFGAA TNTQSPFGTI QNTSTSSGTG VSPFGTFGTN 
241:	SNNKSPFSNL QSGAGAGSSP FGTTTSKANN NNNVGSSAFG TTNNQSPFSG GSGGTFGSAS 
301:	NLNKNTNGNF QSSFGNKGFS FGITPQNDAN KVSQSNPSFG QTMPNTDPNI SLKSNGNATS 
361:	FGFGQQQMNA TNVNANTATG KIRFVQGLSS EKDGILELAD LAEETLKIFR ANKFELGLVP 
421:	DIPPPPALVA