Reviewed, UniProtKB/Swiss-Prot P34077 (NIC96_YEAST)

Names and origin

Protein names

Recommended name:
    Nucleoporin NIC96
Alternative name(s):
    Nuclear pore protein NIC96
    96 kDa nucleoporin-interacting component

Gene names

Name:	NIC96
Ordered Locus Names:	YFR002W

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	839 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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. NIC96, which is localized to the core of the NPC and the distal ring of the nuclear basket, is required for de novo assembly of NPCs. It is involved in nuclear GSP1 import.
Subunit structure	The nuclear pore complex (NPC) constitutes the exclusive means of nucleocytoplasmic transport. NPCs allow the passive diffusion of ions and small molecules and the active, nuclear transport receptor-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoparticles (RNPs), and ribosomal subunits across the nuclear envelope. The 55-60 MDa NPC is composed of at least 31 different subunits: ASM4, CDC31, GLE1, GLE2, NDC1, NIC96, NSP1, NUP1, NUP2, NUP100, NUP116, NUP120, NUP133, NUP145, NUP157, NUP159, NUP170, NUP188, NUP192, NUP42, NUP49, NUP53, NUP57, NUP60, NUP82, NUP84, NUP85, POM152, POM34, SEH1 and SEC1. Due to its 8-fold rotational symmetry, all subunits are present with 8 copies or multiples thereof. NIC96 is part of three NPC subcomplexes, interacting with NSP1 of the NUP57 subcomplex (NIC96, NSP1, NUP49, NUP57), with NUP120 of the NUP84 subcomplex (SEH1,NUP85, NUP120, NUP145C, SEC13, NUP84, NUP133), and with NUP53 of the NUP53-NUP59-NUP170 subcomplex. The interaction with NUP53 is cell cycle dependent. NIC96 is also associated with the distal ring of the nuclear basket and interacts here with MLP2, which forms together with MLP1 nuclear pore-attached intranuclear filaments.
Subcellular location	Nucleus › nuclear pore complex. Nucleus membrane; Peripheral membrane protein; Cytoplasmic side. Nucleus membrane; Peripheral membrane protein; Nucleoplasmic side. Note= Symmetric distribution.
Miscellaneous	Present with 15500 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the nucleoporin interacting component (NIC) family.

Ontologies

Keywords
Biological process	Protein transport Translocation Transport mRNA transport
Cellular component	Membrane Nuclear pore complex Nucleus
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	NLS-bearing substrate import into nucleus Traceable author statement. Source: SGD mRNA export from nucleus Traceable author statement. Source: SGD mRNA-binding (hnRNP) protein import into nucleus Traceable author statement. Source: SGD nuclear pore organization and biogenesis Inferred from mutant phenotype. Source: SGD protein export from nucleus Traceable author statement. Source: SGD rRNA export from nucleus Traceable author statement. Source: SGD ribosomal protein import into nucleus Traceable author statement. Source: SGD snRNA export from nucleus Traceable author statement. Source: SGD snRNP protein import into nucleus Traceable author statement. Source: SGD tRNA export from nucleus Traceable author statement. Source: SGD
Cellular component	nuclear pore Inferred from direct assay. Source: SGD
Molecular function	protein binding Inferred from physical interaction. Source: IntAct structural molecule activity Traceable author statement. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
NUP116	Q02630	1	EBI-12056,EBI-11703
NUP57	P48837	1	EBI-12056,EBI-12324

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view
Molecule processing
	Chain	1 – 839	839	Nucleoporin NIC96
Regions
	Region	25 – 60	36	Leucine zipper-like heptad repeat, required for interaction with NSP1
	Compositional bias	187 – 236	50	Asn-rich
Amino acid modifications
	Modified residue	198	1	Phosphoserine
Experimental info
	Sequence conflict	59	1	Missing in CAA51427. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P34077-1 [UniParc]. Last modified November 1, 1995. Version 2. Checksum: 48EC3BC71281CB44	FASTA	839	96,174
	10 20 30 40 50 60 MLETLRGNKL HSGTSKGANK KLNELLESSD NLPSASSELG SIQVSINELR RRVFQLRSKN 70 80 90 100 110 120 KASKDYTKAH YLLANSGLSF EDVDAFIKDL QTNQFLEPNP PKIIESEELE FYIRTKKEEN 130 140 150 160 170 180 ILMSIEQLLN GATKDFDNFI NHNLNLDWAQ HKNEVMKNFG ILIQDKKTVD HKKSISSLDP 190 200 210 220 230 240 KLPSWGNKGN NILNSNESRL NVNENNILRE KFENYARIVF QFNNSRQANG NFDIANEFIS 250 260 270 280 290 300 ILSSANGTRN AQLLESWKIL ESMKSKDINI VEVGKQYLEQ QFLQYTDNLY KKNMNEGLAT 310 320 330 340 350 360 NVNKIKSFID TKLKKADKSW KISNLTVING VPIWALIFYL LRAGLIKEAL QVLVENKANI 370 380 390 400 410 420 KKVEQSFLTY FKAYASSKDH GLPVEYSTKL HTEYNQHIKS SLDGDPYRLA VYKLIGRCDL 430 440 450 460 470 480 SRKNIPAVTL SIEDWLWMHL MLIKEKDAEN DPVYERYSLE DFQNIIISYG PSRFSNYYLQ 490 500 510 520 530 540 TLLLSGLYGL AIDYTYTFSE MDAVHLAIGL ASLKLFKIDS STRLTKKPKR DIRFANILAN 550 560 570 580 590 600 YTKSFRYSDP RVAVEYLVLI TLNEGPTDVE LCHEALRELV LETKEFTVLL GKIGRDGARI 610 620 630 640 650 660 PGVIEERQPL LHVRDEKEFL HTITEQAARR ADEDGRIYDS ILLYQLAEEY DIVITLVNSL 670 680 690 700 710 720 LSDTLSASDL DQPLVGPDDN SETNPVLLAR RMASIYFDNA GISRQIHVKN KEICMLLLNI 730 740 750 760 770 780 SSIRELYFNK QWQETLSQME LLDLLPFSDE LSARKKAQDF SNLDDNIVKN IPNLLIITLS 790 800 810 820 830 CISNMIHILN ESKYQSSTKG QQIDSLKNVA RQCMIYAGMI QYRMPRETYS TLINIDVSL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Purification of NSP1 reveals complex formation with 'GLFG' nucleoporins and a novel nuclear pore protein NIC96." Grandi P., Doye V., Hurt E.C. EMBO J. 12:3061-3071(1993) [PubMed: 7688296] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
[2]	"Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae." Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S., Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K., Yamazaki M., Tashiro H., Eki T. Nat. Genet. 10:261-268(1995) [PubMed: 7670463] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"Sequencing of a 23 kb fragment from Saccharomyces cerevisiae chromosome VI." Naitou M., Ozawa M., Sasanuma S., Kobayashi M., Hagiwara H., Shibata T., Hanaoka F., Watanabe K., Ono A., Yamazaki M., Tashiro H., Eki T., Murakami Y. Yeast 12:77-84(1996) [PubMed: 8789262] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-591. Strain: ATCC 204511 / S288c / AB972.
[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., Rout M.P., Marelli M., Blobel G., Wozniak R.W. J. Cell Biol. 131:1133-1148(1995) [PubMed: 8522578] [Abstract] Cited for: PROTEIN SEQUENCE OF 104-116 AND 277-291.
[5]	"Functional interaction of Nic96p with a core nucleoporin complex consisting of Nsp1p, Nup49p and a novel protein Nup57p." Grandi P., Schlaich N.L., Tekotte H., Hurt E.C. EMBO J. 14:76-87(1995) [PubMed: 7828598] [Abstract] Cited for: FUNCTION, HEPTAD REPEAT DEPENDENT INTERACTION WITH NSP1.
[6]	"Nic96p is required for nuclear pore formation and functionally interacts with a novel nucleoporin, Nup188p." Zabel U., Doye V., Tekotte H., Wepf R., Grandi P., Hurt E.C. J. Cell Biol. 133:1141-1152(1996) [PubMed: 8682854] [Abstract] Cited for: INTERACTION WITH NUP188.
[7]	"The yeast nucleoporin Nup188p interacts genetically and physically with the core structures of the nuclear pore complex." Nehrbass U., Rout M.P., Maguire S., Blobel G., Wozniak R.W. J. Cell Biol. 133:1153-1162(1996) [PubMed: 8682855] [Abstract] Cited for: FUNCTION, INTERACTION WITH NUP188.
[8]	"In vitro reconstitution of a heterotrimeric nucleoporin complex consisting of recombinant Nsp1p, Nup49p, and Nup57p." Schlaich N.L., Haener M., Lustig A., Aebi U., Hurt E.C. Mol. Biol. Cell 8:33-46(1997) [PubMed: 9017593] [Abstract] Cited for: FUNCTION, INTERACTION WITH NUP57 SUBCOMPLEX.
[9]	"Nup192p is a conserved nucleoporin with a preferential location at the inner site of the nuclear membrane." Kosova B., Pante N., Rollenhagen C., Hurt E.C. J. Biol. Chem. 274:22646-22651(1999) [PubMed: 10428845] [Abstract] Cited for: FUNCTION, INTERACTION WITH NUP192.
[10]	"Mlp2p, a component of nuclear pore attached intranuclear filaments, associates with nic96p." Kosova B., Pante N., Rollenhagen C., Podtelejnikov A., Mann M., Aebi U., Hurt E.C. J. Biol. Chem. 275:343-350(2000) [PubMed: 10617624] [Abstract] Cited for: FUNCTION, INTERACTION WITH MLP2.
[11]	"The yeast nuclear pore complex: composition, architecture, and transport mechanism." Rout M.P., Aitchison J.D., Suprapto A., Hjertaas K., Zhao Y., Chait B.T. J. Cell Biol. 148:635-651(2000) [PubMed: 10684247] [Abstract] Cited for: CHARACTERIZATION, NPC SUBUNIT LOCATION.
[12]	"Yeast nuclear pore complex assembly defects determined by nuclear envelope reconstruction." Gomez-Ospina N., Morgan G., Giddings T.H. Jr., Kosova B., Hurt E.C., Winey M. J. Struct. Biol. 132:1-5(2000) [PubMed: 11121302] [Abstract] Cited for: FUNCTION, NPC DE NOVO ASSEMBLY.
[13]	"Comparative spatial localization of protein-A-tagged and authentic yeast nuclear pore complex proteins by immunogold electron microscopy." Fahrenkrog B., Aris J.P., Hurt E.C., Pante N., Aebi U. J. Struct. Biol. 129:295-305(2000) [PubMed: 10806080] [Abstract] Cited for: FUNCTION, LOCATION WITHIN THE NPC.
[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., Balduf C., Hurt E.C. Mol. Cell. Biol. 21:7944-7955(2001) [PubMed: 11689687] [Abstract] Cited for: FUNCTION, INTERACTION WITH NSP1 COILED COIL.
[15]	"Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes." Lusk C.P., Makhnevych T., Marelli M., Aitchison J.D., Wozniak R.W. J. Cell Biol. 159:267-278(2002) [PubMed: 12403813] [Abstract] Cited for: FUNCTION, INTERACTION WITH NUP53.
[16]	"In situ analysis of spatial relationships between proteins of the nuclear pore complex." Damelin M., Silver P.A. Biophys. J. 83:3626-3636(2002) [PubMed: 12496130] [Abstract] Cited for: FUNCTION, INTERACTION WITH NUP53 AND NUP120.
[17]	"Nuclear accumulation of the small GTPase Gsp1p depends on nucleoporins Nup133p, Rat2p/Nup120p, Nup85p, Nic96p, and the acetyl-CoA carboxylase Acc1p." Gao H., Sumanaweera N., Bailer S.M., Stochaj U. J. Biol. Chem. 278:25331-25340(2003) [PubMed: 12730220] [Abstract] Cited for: FUNCTION, NUCLEAR GSP1 IMPORT.
[18]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[19]	"Peering through the pore: nuclear pore complex structure, assembly, and function." Suntharalingam M., Wente S.R. Dev. Cell 4:775-789(2003) [PubMed: 12791264] [Abstract] Cited for: REVIEW.
[20]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-198, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X72923 Genomic DNA. Translation: CAA51427.1.
D50617 Genomic DNA. Translation: BAA09241.1.

PIR

S35319.

RefSeq

NP_116657.1.

3D structure databases

PDBMSD

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2QX5	X-ray	2.50	A/B	186-839	[»]
2RFO	X-ray	2.60	A/B	189-839	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:745N.

IntAct

P34077.

Proteomic databases

PeptideAtlas

P34077.

Genome annotation databases

Ensembl

YFR002W. Saccharomyces cerevisiae. [Contig view]

GeneID

850552.

GenomeReviews

Gene locus YFR002W in contig D50617_GR.

KEGG

sce:YFR002W.

NMPDR

fig|4932.3.peg.2288.

Organism-specific databases

CYGD

YFR002w.

SGD

S000001898. NIC96.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P34077.

Gene expression databases

ArrayExpress

P34077.

GermOnline

YFR002W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR007231. Nucleoporin_intact_comp.
[Graphical view]

PANTHER

PTHR11225. NIC. 1 hit.

Pfam

PF04097. NIC. 1 hit.
[Graphical view]

ProDom

P34077.
[Graphical view] [Entries sharing at least one domain]

BLOCKS

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Other Resources

LinkHub

P34077.

ProtoNet

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Entry information

Entry name

NIC96_YEAST

Accession

Primary (citable) accession number: P34077

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	November 1, 1995
Last modified:	September 2, 2008
This is version 79 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)