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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:Q03790
Protein Name:Nucleoporin NUP53
Length:475
Molecular Weight:52619.00
Species:Saccharomyces cerevisiae (Baker's yeast) [4932]
Number of TMSs:1
Location1 / Topology2 / Orientation3: Nucleus1 / Peripheral membrane protein2 / Cytoplasmic side3
Substrate

Cross database links:

DIP: DIP-1467N DIP-1467N DIP-1467N DIP-1467N
RefSeq: NP_013873.1   
Entrez Gene ID: 855184   
Pfam: PF05172   
KEGG: sce:YMR153W    sce:YMR153W    sce:YMR153W    sce:YMR153W   

Gene Ontology

GO:0031015 C:karyopherin docking complex
GO:0031965 C:nuclear membrane
GO:0042802 F:identical protein binding
GO:0005198 F:structural molecule activity
GO:0051301 P:cell division
GO:0007067 P:mitosis
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:0000059 P:protein import into nucleus, docking
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:0005643 C:nuclear pore
GO:0005543 F:phospholipid binding
GO:0003697 F:single-stranded DNA binding
GO:0051028 P:mRNA transport
GO:0007088 P:regulation of mitosis
GO:0060188 P:regulation of protein desumoylation

References (60)

[1] “The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.”  Bowman S.et.al.   9169872
[2] “Specific binding of the karyopherin Kap121p to a subunit of the nuclear pore complex containing Nup53p, Nup59p, and Nup170p.”  Marelli M.et.al.   9864357
[3] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[4] “A link between the synthesis of nucleoporins and the biogenesis of the nuclear envelope.”  Marelli M.et.al.   11352933
[5] “Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes.”  Lusk C.P.et.al.   12403813
[6] “The yeast nuclear pore complex functionally interacts with components of the spindle assembly checkpoint.”  Iouk T.et.al.   12473689
[7] “Cell cycle regulated transport controlled by alterations in the nuclear pore complex.”  Makhnevych T.et.al.   14697200
[8] “Global analysis of protein expression in yeast.”  Ghaemmaghami S.et.al.   14562106
[9] “Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.”  Denning D.P.et.al.   12604785
[10] “A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.”  Uetz P.et.al.   10688190
[11] “A comprehensive two-hybrid analysis to explore the yeast protein interactome.”  Ito T.et.al.   11283351
[12] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[13] “Targets of the cyclin-dependent kinase Cdk1.”  Ubersax J.A.et.al.   14574415
[14] “Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.”  Smolka M.B.et.al.   17563356
[15] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[16] “The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.”  Bowman S.et.al.   9169872
[17] “Specific binding of the karyopherin Kap121p to a subunit of the nuclear pore complex containing Nup53p, Nup59p, and Nup170p.”  Marelli M.et.al.   9864357
[18] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[19] “A link between the synthesis of nucleoporins and the biogenesis of the nuclear envelope.”  Marelli M.et.al.   11352933
[20] “Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes.”  Lusk C.P.et.al.   12403813
[21] “The yeast nuclear pore complex functionally interacts with components of the spindle assembly checkpoint.”  Iouk T.et.al.   12473689
[22] “Cell cycle regulated transport controlled by alterations in the nuclear pore complex.”  Makhnevych T.et.al.   14697200
[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] “A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.”  Uetz P.et.al.   10688190
[26] “A comprehensive two-hybrid analysis to explore the yeast protein interactome.”  Ito T.et.al.   11283351
[27] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[28] “Targets of the cyclin-dependent kinase Cdk1.”  Ubersax J.A.et.al.   14574415
[29] “Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.”  Smolka M.B.et.al.   17563356
[30] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[31] “The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.”  Bowman S.et.al.   9169872
[32] “Specific binding of the karyopherin Kap121p to a subunit of the nuclear pore complex containing Nup53p, Nup59p, and Nup170p.”  Marelli M.et.al.   9864357
[33] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[34] “A link between the synthesis of nucleoporins and the biogenesis of the nuclear envelope.”  Marelli M.et.al.   11352933
[35] “Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes.”  Lusk C.P.et.al.   12403813
[36] “The yeast nuclear pore complex functionally interacts with components of the spindle assembly checkpoint.”  Iouk T.et.al.   12473689
[37] “Cell cycle regulated transport controlled by alterations in the nuclear pore complex.”  Makhnevych T.et.al.   14697200
[38] “Global analysis of protein expression in yeast.”  Ghaemmaghami S.et.al.   14562106
[39] “Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.”  Denning D.P.et.al.   12604785
[40] “A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.”  Uetz P.et.al.   10688190
[41] “A comprehensive two-hybrid analysis to explore the yeast protein interactome.”  Ito T.et.al.   11283351
[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] “Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.”  Smolka M.B.et.al.   17563356
[45] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[46] “The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.”  Bowman S.et.al.   9169872
[47] “Specific binding of the karyopherin Kap121p to a subunit of the nuclear pore complex containing Nup53p, Nup59p, and Nup170p.”  Marelli M.et.al.   9864357
[48] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[49] “A link between the synthesis of nucleoporins and the biogenesis of the nuclear envelope.”  Marelli M.et.al.   11352933
[50] “Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes.”  Lusk C.P.et.al.   12403813
[51] “The yeast nuclear pore complex functionally interacts with components of the spindle assembly checkpoint.”  Iouk T.et.al.   12473689
[52] “Cell cycle regulated transport controlled by alterations in the nuclear pore complex.”  Makhnevych T.et.al.   14697200
[53] “Global analysis of protein expression in yeast.”  Ghaemmaghami S.et.al.   14562106
[54] “Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.”  Denning D.P.et.al.   12604785
[55] “A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.”  Uetz P.et.al.   10688190
[56] “A comprehensive two-hybrid analysis to explore the yeast protein interactome.”  Ito T.et.al.   11283351
[57] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[58] “Targets of the cyclin-dependent kinase Cdk1.”  Ubersax J.A.et.al.   14574415
[59] “Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.”  Smolka M.B.et.al.   17563356
[60] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
Structure:
3W3Y   5UAZ     

External Searches:

Analyze:

Predict TMSs (Predict number of transmembrane segments)
Window Size: Angle:  
FASTA formatted sequence
1:	MADLQKQENS SRFTNVSVIA PESQGQHEQQ KQQEQLEQQK QPTGLLKGLN GFPSAPQPLF 
61:	MEDPPSTVSG ELNDNPAWFN NPRKRAIPNS IIKRSNGQSL SPVRSDSADV PAFSNSNGFN 
121:	NVTFGSKKDP RILKNVSPND NNSANNNAHS SDLGTVVFDS NEAPPKTSLA DWQKEDGIFS 
181:	SKTDNIEDPN LSSNITFDGK PTATPSPFRP LEKTSRILNF FDKNTKTTPN TASSEASAGS 
241:	KEGASTNWDD HAIIIFGYPE TIANSIILHF ANFGEILEDF RVIKDFKKLN SKNMSKSPSL 
301:	TAQKYPIYTG DGWVKLTYKS ELSKSRALQE NGIIMNGTLI GCVSYSPAAL KQLASLKKSE 
361:	EIINNKTSSQ TSLSSKDLSN YRKTEGIFEK AKAKAVTSKV RNAEFKVSKN STSFKNPRRL 
421:	EIKDGRSLFL RNRGKIHSGV LSSIESDLKK REQASKSKKS WLNRLNNWLF GWNDL