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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:P34077
Protein Name:Nucleoporin NIC96
Length:839
Molecular Weight:96174.00
Species:Saccharomyces cerevisiae (Baker's yeast) [4932]
Location1 / Topology2 / Orientation3: Nucleus1 / Peripheral membrane protein2 / Cytoplasmic side3
Substrate

Cross database links:

DIP: DIP-745N DIP-745N DIP-745N DIP-745N
RefSeq: NP_116657.1   
Entrez Gene ID: 850552   
Pfam: PF04097   
KEGG: sce:YFR002W    sce:YFR002W    sce:YFR002W    sce:YFR002W   

Gene Ontology

GO:0055125 C:Nic96 complex
GO:0031965 C:nuclear membrane
GO:0005515 F: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:0051028 P:mRNA transport
GO:0006606 P:protein import into nucleus
GO:0000055 P:ribosomal large subunit export from nucleus

References (80)

[1] “Purification of NSP1 reveals complex formation with 'GLFG' nucleoporins and a novel nuclear pore protein NIC96.”  Grandi P.et.al.   7688296
[2] “Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae.”  Murakami Y.et.al.   7670463
[3] “Sequencing of a 23 kb fragment from Saccharomyces cerevisiae chromosome VI.”  Naitou M.et.al.   8789262
[4] “Two novel related yeast nucleoporins Nup170p and Nup157p: complementation with the vertebrate homologue Nup155p and functional interactions with the yeast nuclear pore-membrane protein Pom152p.”  Aitchison J.D.et.al.   8522578
[5] “Functional interaction of Nic96p with a core nucleoporin complex consisting of Nsp1p, Nup49p and a novel protein Nup57p.”  Grandi P.et.al.   7828598
[6] “Nic96p is required for nuclear pore formation and functionally interacts with a novel nucleoporin, Nup188p.”  Zabel U.et.al.   8682854
[7] “The yeast nucleoporin Nup188p interacts genetically and physically with the core structures of the nuclear pore complex.”  Nehrbass U.et.al.   8682855
[8] “In vitro reconstitution of a heterotrimeric nucleoporin complex consisting of recombinant Nsp1p, Nup49p, and Nup57p.”  Schlaich N.L.et.al.   9017593
[9] “Nup192p is a conserved nucleoporin with a preferential location at the inner site of the nuclear membrane.”  Kosova B.et.al.   10428845
[10] “Mlp2p, a component of nuclear pore attached intranuclear filaments, associates with nic96p.”  Kosova B.et.al.   10617624
[11] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[12] “Yeast nuclear pore complex assembly defects determined by nuclear envelope reconstruction.”  Gomez-Ospina N.et.al.   11121302
[13] “Comparative spatial localization of protein-A-tagged and authentic yeast nuclear pore complex proteins by immunogold electron microscopy.”  Fahrenkrog B.et.al.   10806080
[14] “The Nsp1p carboxy-terminal domain is organized into functionally distinct coiled-coil regions required for assembly of nucleoporin subcomplexes and nucleocytoplasmic transport.”  Bailer S.M.et.al.   11689687
[15] “Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes.”  Lusk C.P.et.al.   12403813
[16] “In situ analysis of spatial relationships between proteins of the nuclear pore complex.”  Damelin M.et.al.   12496130
[17] “Nuclear accumulation of the small GTPase Gsp1p depends on nucleoporins Nup133p, Rat2p/Nup120p, Nup85p, Nic96p, and the acetyl-CoA carboxylase Acc1p.”  Gao H.et.al.   12730220
[18] “Global analysis of protein expression in yeast.”  Ghaemmaghami S.et.al.   14562106
[19] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[20] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[21] “Purification of NSP1 reveals complex formation with 'GLFG' nucleoporins and a novel nuclear pore protein NIC96.”  Grandi P.et.al.   7688296
[22] “Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae.”  Murakami Y.et.al.   7670463
[23] “Sequencing of a 23 kb fragment from Saccharomyces cerevisiae chromosome VI.”  Naitou M.et.al.   8789262
[24] “Two novel related yeast nucleoporins Nup170p and Nup157p: complementation with the vertebrate homologue Nup155p and functional interactions with the yeast nuclear pore-membrane protein Pom152p.”  Aitchison J.D.et.al.   8522578
[25] “Functional interaction of Nic96p with a core nucleoporin complex consisting of Nsp1p, Nup49p and a novel protein Nup57p.”  Grandi P.et.al.   7828598
[26] “Nic96p is required for nuclear pore formation and functionally interacts with a novel nucleoporin, Nup188p.”  Zabel U.et.al.   8682854
[27] “The yeast nucleoporin Nup188p interacts genetically and physically with the core structures of the nuclear pore complex.”  Nehrbass U.et.al.   8682855
[28] “In vitro reconstitution of a heterotrimeric nucleoporin complex consisting of recombinant Nsp1p, Nup49p, and Nup57p.”  Schlaich N.L.et.al.   9017593
[29] “Nup192p is a conserved nucleoporin with a preferential location at the inner site of the nuclear membrane.”  Kosova B.et.al.   10428845
[30] “Mlp2p, a component of nuclear pore attached intranuclear filaments, associates with nic96p.”  Kosova B.et.al.   10617624
[31] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[32] “Yeast nuclear pore complex assembly defects determined by nuclear envelope reconstruction.”  Gomez-Ospina N.et.al.   11121302
[33] “Comparative spatial localization of protein-A-tagged and authentic yeast nuclear pore complex proteins by immunogold electron microscopy.”  Fahrenkrog B.et.al.   10806080
[34] “The Nsp1p carboxy-terminal domain is organized into functionally distinct coiled-coil regions required for assembly of nucleoporin subcomplexes and nucleocytoplasmic transport.”  Bailer S.M.et.al.   11689687
[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] “In situ analysis of spatial relationships between proteins of the nuclear pore complex.”  Damelin M.et.al.   12496130
[37] “Nuclear accumulation of the small GTPase Gsp1p depends on nucleoporins Nup133p, Rat2p/Nup120p, Nup85p, Nic96p, and the acetyl-CoA carboxylase Acc1p.”  Gao H.et.al.   12730220
[38] “Global analysis of protein expression in yeast.”  Ghaemmaghami S.et.al.   14562106
[39] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[40] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[41] “Purification of NSP1 reveals complex formation with 'GLFG' nucleoporins and a novel nuclear pore protein NIC96.”  Grandi P.et.al.   7688296
[42] “Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae.”  Murakami Y.et.al.   7670463
[43] “Sequencing of a 23 kb fragment from Saccharomyces cerevisiae chromosome VI.”  Naitou M.et.al.   8789262
[44] “Two novel related yeast nucleoporins Nup170p and Nup157p: complementation with the vertebrate homologue Nup155p and functional interactions with the yeast nuclear pore-membrane protein Pom152p.”  Aitchison J.D.et.al.   8522578
[45] “Functional interaction of Nic96p with a core nucleoporin complex consisting of Nsp1p, Nup49p and a novel protein Nup57p.”  Grandi P.et.al.   7828598
[46] “Nic96p is required for nuclear pore formation and functionally interacts with a novel nucleoporin, Nup188p.”  Zabel U.et.al.   8682854
[47] “The yeast nucleoporin Nup188p interacts genetically and physically with the core structures of the nuclear pore complex.”  Nehrbass U.et.al.   8682855
[48] “In vitro reconstitution of a heterotrimeric nucleoporin complex consisting of recombinant Nsp1p, Nup49p, and Nup57p.”  Schlaich N.L.et.al.   9017593
[49] “Nup192p is a conserved nucleoporin with a preferential location at the inner site of the nuclear membrane.”  Kosova B.et.al.   10428845
[50] “Mlp2p, a component of nuclear pore attached intranuclear filaments, associates with nic96p.”  Kosova B.et.al.   10617624
[51] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[52] “Yeast nuclear pore complex assembly defects determined by nuclear envelope reconstruction.”  Gomez-Ospina N.et.al.   11121302
[53] “Comparative spatial localization of protein-A-tagged and authentic yeast nuclear pore complex proteins by immunogold electron microscopy.”  Fahrenkrog B.et.al.   10806080
[54] “The Nsp1p carboxy-terminal domain is organized into functionally distinct coiled-coil regions required for assembly of nucleoporin subcomplexes and nucleocytoplasmic transport.”  Bailer S.M.et.al.   11689687
[55] “Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes.”  Lusk C.P.et.al.   12403813
[56] “In situ analysis of spatial relationships between proteins of the nuclear pore complex.”  Damelin M.et.al.   12496130
[57] “Nuclear accumulation of the small GTPase Gsp1p depends on nucleoporins Nup133p, Rat2p/Nup120p, Nup85p, Nic96p, and the acetyl-CoA carboxylase Acc1p.”  Gao H.et.al.   12730220
[58] “Global analysis of protein expression in yeast.”  Ghaemmaghami S.et.al.   14562106
[59] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[60] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
[61] “Purification of NSP1 reveals complex formation with 'GLFG' nucleoporins and a novel nuclear pore protein NIC96.”  Grandi P.et.al.   7688296
[62] “Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae.”  Murakami Y.et.al.   7670463
[63] “Sequencing of a 23 kb fragment from Saccharomyces cerevisiae chromosome VI.”  Naitou M.et.al.   8789262
[64] “Two novel related yeast nucleoporins Nup170p and Nup157p: complementation with the vertebrate homologue Nup155p and functional interactions with the yeast nuclear pore-membrane protein Pom152p.”  Aitchison J.D.et.al.   8522578
[65] “Functional interaction of Nic96p with a core nucleoporin complex consisting of Nsp1p, Nup49p and a novel protein Nup57p.”  Grandi P.et.al.   7828598
[66] “Nic96p is required for nuclear pore formation and functionally interacts with a novel nucleoporin, Nup188p.”  Zabel U.et.al.   8682854
[67] “The yeast nucleoporin Nup188p interacts genetically and physically with the core structures of the nuclear pore complex.”  Nehrbass U.et.al.   8682855
[68] “In vitro reconstitution of a heterotrimeric nucleoporin complex consisting of recombinant Nsp1p, Nup49p, and Nup57p.”  Schlaich N.L.et.al.   9017593
[69] “Nup192p is a conserved nucleoporin with a preferential location at the inner site of the nuclear membrane.”  Kosova B.et.al.   10428845
[70] “Mlp2p, a component of nuclear pore attached intranuclear filaments, associates with nic96p.”  Kosova B.et.al.   10617624
[71] “The yeast nuclear pore complex: composition, architecture, and transport mechanism.”  Rout M.P.et.al.   10684247
[72] “Yeast nuclear pore complex assembly defects determined by nuclear envelope reconstruction.”  Gomez-Ospina N.et.al.   11121302
[73] “Comparative spatial localization of protein-A-tagged and authentic yeast nuclear pore complex proteins by immunogold electron microscopy.”  Fahrenkrog B.et.al.   10806080
[74] “The Nsp1p carboxy-terminal domain is organized into functionally distinct coiled-coil regions required for assembly of nucleoporin subcomplexes and nucleocytoplasmic transport.”  Bailer S.M.et.al.   11689687
[75] “Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes.”  Lusk C.P.et.al.   12403813
[76] “In situ analysis of spatial relationships between proteins of the nuclear pore complex.”  Damelin M.et.al.   12496130
[77] “Nuclear accumulation of the small GTPase Gsp1p depends on nucleoporins Nup133p, Rat2p/Nup120p, Nup85p, Nic96p, and the acetyl-CoA carboxylase Acc1p.”  Gao H.et.al.   12730220
[78] “Global analysis of protein expression in yeast.”  Ghaemmaghami S.et.al.   14562106
[79] “Peering through the pore: nuclear pore complex structure, assembly, and function.”  Suntharalingam M.et.al.   12791264
[80] “A multidimensional chromatography technology for in-depth phosphoproteome analysis.”  Albuquerque C.P.et.al.   18407956
Structure:
2QX5   2RFO     

External Searches:

Analyze:

Predict TMSs (Predict number of transmembrane segments)
Window Size: Angle:  
FASTA formatted sequence
1:	MLETLRGNKL HSGTSKGANK KLNELLESSD NLPSASSELG SIQVSINELR RRVFQLRSKN 
61:	KASKDYTKAH YLLANSGLSF EDVDAFIKDL QTNQFLEPNP PKIIESEELE FYIRTKKEEN 
121:	ILMSIEQLLN GATKDFDNFI NHNLNLDWAQ HKNEVMKNFG ILIQDKKTVD HKKSISSLDP 
181:	KLPSWGNKGN NILNSNESRL NVNENNILRE KFENYARIVF QFNNSRQANG NFDIANEFIS 
241:	ILSSANGTRN AQLLESWKIL ESMKSKDINI VEVGKQYLEQ QFLQYTDNLY KKNMNEGLAT 
301:	NVNKIKSFID TKLKKADKSW KISNLTVING VPIWALIFYL LRAGLIKEAL QVLVENKANI 
361:	KKVEQSFLTY FKAYASSKDH GLPVEYSTKL HTEYNQHIKS SLDGDPYRLA VYKLIGRCDL 
421:	SRKNIPAVTL SIEDWLWMHL MLIKEKDAEN DPVYERYSLE DFQNIIISYG PSRFSNYYLQ 
481:	TLLLSGLYGL AIDYTYTFSE MDAVHLAIGL ASLKLFKIDS STRLTKKPKR DIRFANILAN 
541:	YTKSFRYSDP RVAVEYLVLI TLNEGPTDVE LCHEALRELV LETKEFTVLL GKIGRDGARI 
601:	PGVIEERQPL LHVRDEKEFL HTITEQAARR ADEDGRIYDS ILLYQLAEEY DIVITLVNSL 
661:	LSDTLSASDL DQPLVGPDDN SETNPVLLAR RMASIYFDNA GISRQIHVKN KEICMLLLNI 
721:	SSIRELYFNK QWQETLSQME LLDLLPFSDE LSARKKAQDF SNLDDNIVKN IPNLLIITLS 
781:	CISNMIHILN ESKYQSSTKG QQIDSLKNVA RQCMIYAGMI QYRMPRETYS TLINIDVSL