P32497 (EIF3C_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Eukaryotic translation initiation factor 3 subunit C
Short name=eIF3c

Alternative name(s):
Eukaryotic translation initiation factor 3 93 kDa subunit
Short name=eIF3 p93
Nuclear transport protein NIP1
Translation initiation factor eIF3, p93 subunit

Gene names

Name:	NIP1
Ordered Locus Names:	YMR309C
ORF Names:	YM9924.01C, YM9952.11C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	812 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. Ref.9
Subunit structure	The eukaryotic translation initiation factor 3 (eIF-3) core complex is composed of TIF32, PRT1, NIP1, TIF34 and TIF35. A subcomplex of TIF32, NIP1 and PRT1 mediates the interaction with eIF-1, TIF5/eIF-5 and HCR1. The factors eIF-1, eIF-2, eIF-3, TIF5/eIF-5 and methionyl-tRNAi form a multifactor complex (MFC) that may bind to the 40S ribosome. TIF32, NIP1 and TIF5/eIF-5 comprise a minimal 40S-ribosome-binding unit. NIP1 interacts with TIF5/eIF-5 and SUI1. Ref.4 Ref.5 Ref.6 Ref.7 Ref.9 Ref.11 Ref.16
Subcellular location	Cytoplasm. Note: Mainly cytoplasmic. Ref.1
Miscellaneous	Present with 78900 molecules/cell in log phase SD medium. HAMAP-Rule MF_03002
Sequence similarities	Belongs to the eIF-3 subunit C family. Contains 1 PCI domain.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Molecular function	Initiation factor
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Cellular_component	cytoplasmic stress granule Inferred from direct assay PubMed 19470581. Source: SGD eukaryotic translation initiation factor 3 complex Inferred from direct assay PubMed 9660829. Source: SGD multi-eIF complex Inferred from direct assay PubMed 11018020. Source: SGD
Molecular_function	translation initiation factor activity Inferred from direct assay Ref.6. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PRT1	P06103	7	EBI-8965,EBI-8973
RPB4	P20433	5	EBI-8965,EBI-15777
TIF5	P38431	5	EBI-8965,EBI-9038

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 812	812	Eukaryotic translation initiation factor 3 subunit C HAMAP-Rule MF_03002		PRO_0000123530
Regions
	Domain	650 – 780	131	PCI
	Compositional bias	15 – 147	133	Asp/Glu-rich (acidic) HAMAP-Rule MF_03002
	Compositional bias	15 – 36	22	Ser-rich HAMAP-Rule MF_03002
Amino acid modifications
	Modified residue	98	1	Phosphoserine Ref.8 Ref.12 Ref.14 Ref.15
	Modified residue	99	1	Phosphoserine Ref.8 Ref.12 Ref.14 Ref.15
	Modified residue	103	1	Phosphoserine Ref.8 Ref.12 Ref.14 Ref.15
	Modified residue	809	1	Phosphoserine Ref.13
Experimental info
	Sequence conflict	111	1	V → D in L02899. Ref.1
	Sequence conflict	583	1	Q → H in L02899. Ref.1
	Sequence conflict	641	1	K → N in L02899. Ref.1
	Sequence conflict	643	1	K → N in L02899. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P32497 [UniParc]. Last modified October 1, 1996. Version 2. Checksum: EE05097C44C45A4C	FASTA	812	93,204
	10 20 30 40 50 60 MSRFFSSNYE YDVASSSSEE DLLSSSEEDL LSSSSSESEL DQESDDSFFN ESESESEADV 70 80 90 100 110 120 DSDDSDAKPY GPDWFKKSEF RKQGGGSNKF LKSSNYDSSD EESDEEDGKK VVKSAKEKLL 130 140 150 160 170 180 DEMQDVYNKI SQAENSDDWL TISNEFDLIS RLLVRAQQQN WGTPNIFIKV VAQVEDAVNN 190 200 210 220 230 240 TQQADLKNKA VARAYNTTKQ RVKKVSRENE DSMAKFRNDP ESFDKEPTAD LDISANGFTI 250 260 270 280 290 300 SSSQGNDQAV QEDFFTRLQT IIDSRGKKTV NQQSLISTLE ELLTVAEKPY EFIMAYLTLI 310 320 330 340 350 360 PSRFDASANL SYQPIDQWKS SFNDISKLLS ILDQTIDTYQ VNEFADPIDF IEDEPKEDSD 370 380 390 400 410 420 GVKRILGSIF SFVERLDDEF MKSLLNIDPH SSDYLIRLRD EQSIYNLILR TQLYFEATLK 430 440 450 460 470 480 DEHDLERALT RPFVKRLDHI YYKSENLIKI METAAWNIIP AQFKSKFTSK DQLDSADYVD 490 500 510 520 530 540 NLIDGLSTIL SKQNNIAVQK RAILYNIYYT ALNKDFQTAK DMLLTSQVQT NINQFDSSLQ 550 560 570 580 590 600 ILFNRVVVQL GLSAFKLCLI EECHQILNDL LSSSHLREIL GQQSLHRISL NSSNNASADE 610 620 630 640 650 660 RARQCLPYHQ HINLDLIDVV FLTCSLLIEI PRMTAFYSGI KVKRIPYSPK SIRRSLEHYD 670 680 690 700 710 720 KLSFQGPPET LRDYVLFAAK SMQKGNWRDS VKYLREIKSW ALLPNMETVL NSLTERVQVE 730 740 750 760 770 780 SLKTYFFSFK RFYSSFSVAK LAELFDLPEN KVVEVLQSVI AELEIPAKLN DEKTIFVVEK 790 800 810 GDEITKLEEA MVKLNKEYKI AKERLNPPSN RR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"NIP1, a gene required for nuclear transport in yeast." Gu Z., Moerschell R.P., Sherman F., Goldfarb D.S. Proc. Natl. Acad. Sci. U.S.A. 89:10355-10359(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUBCELLULAR LOCATION.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII." Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T., Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P. , Skelton J., Walsh S.V., Whitehead S., Barrell B.G. Nature 387:90-93(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Purified yeast translational initiation factor eIF-3 is an RNA-binding protein complex that contains the PRT1 protein." Naranda T., MacMillan S.E., Hershey J.W.B. J. Biol. Chem. 269:32286-32292(1994) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE EIF-3 COMPLEX.
[5]	"Nip1p associates with 40 S ribosomes and the Prt1p subunit of eukaryotic initiation factor 3 and is required for efficient translation initiation." Greenberg J.R., Phan L., Gu Z., deSilva A., Apolito C., Sherman F., Hinnebusch A.G., Goldfarb D.S. J. Biol. Chem. 273:23485-23494(1998) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PRT1, ASSOCIATION WITH 40S RIBOSOMES.
[6]	"Identification of a translation initiation factor 3 (eIF3) core complex, conserved in yeast and mammals, that interacts with eIF5." Phan L., Zhang X., Asano K., Anderson J., Vornlocher H.-P., Greenberg J.R., Qin J., Hinnebusch A.G. Mol. Cell. Biol. 18:4935-4946(1998) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE EIF-3 CORE COMPLEX, MASS SPECTROMETRY, INTERACTION WITH TIF5 AND SUI1.
[7]	"Conserved bipartite motifs in yeast eIF5 and eIF2Bepsilon, GTPase-activating and GDP-GTP exchange factors in translation initiation, mediate binding to their common substrate eIF2." Asano K., Krishnamoorthy T., Phan L., Pavitt G.D., Hinnebusch A.G. EMBO J. 18:1673-1688(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH TIF5.
[8]	"Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae." Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Nat. Biotechnol. 20:301-305(2002) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-98; SER-99 AND SER-103, MASS SPECTROMETRY. Strain: 2124.
[9]	"The yeast eIF3 subunits TIF32/a, NIP1/c, and eIF5 make critical connections with the 40S ribosome in vivo." Valasek L., Mathew A.A., Shin B.-S., Nielsen K.H., Szamecz B., Hinnebusch A.G. Genes Dev. 17:786-799(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, ASSOCIATION WITH THE 40S RIBOSOME, INTERACTION WITH RPS0A.
[10]	"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] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[11]	"Interaction of the RNP1 motif in PRT1 with HCR1 promotes 40S binding of eukaryotic initiation factor 3 in yeast." Nielsen K.H., Valasek L., Sykes C., Jivotovskaya A., Hinnebusch A.G. Mol. Cell. Biol. 26:2984-2998(2006) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PRT1, ASSOCIATION WITH THE 40S RIBOSOME.
[12]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-98; SER-99 AND SER-103, MASS SPECTROMETRY. Strain: ADR376.
[13]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-809, MASS SPECTROMETRY.
[14]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-98; SER-99 AND SER-103, MASS SPECTROMETRY.
[15]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-98; SER-99 AND SER-103, MASS SPECTROMETRY.
[16]	"Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3." Zhou M., Sandercock A.M., Fraser C.S., Ridlova G., Stephens E., Schenauer M.R., Yokoi-Fong T., Barsky D., Leary J.A., Hershey J.W.B., Doudna J.A., Robinson C.V. Proc. Natl. Acad. Sci. U.S.A. 105:18139-18144(2008) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE EIF-3 COMPLEX WITH PRT1; TIF32; TIF34 AND TIF35.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	L02899 Genomic DNA. No translation available. Z54141 Genomic DNA. Translation: CAA90827.1. Z49212 Genomic DNA. Translation: CAA89142.1. BK006946 Genomic DNA. Translation: DAA10210.1.
PIR	A46417.
RefSeq	NP_014040.1. NM_001182820.1.
3D structure databases
ProteinModelPortal	P32497.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-1470N.
IntAct	P32497. 58 interactions.
MINT	MINT-388745.
STRING	4932.YMR309C.
Proteomic databases
PaxDb	P32497.
PeptideAtlas	P32497.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YMR309C; YMR309C; YMR309C.
GeneID	855357.
KEGG	sce:YMR309C.
Organism-specific databases
CYGD	YMR309c.
SGD	S000004926. NIP1.
Phylogenomic databases
eggNOG	NOG305883.
GeneTree	ENSGT00390000017900.
HOGENOM	HOG000029414.
KO	K03252.
OMA	GMITEAH.
OrthoDB	EOG4578FW.
Gene expression databases
Genevestigator	P32497.
GermOnline	YMR309C. Saccharomyces cerevisiae.
Family and domain databases
HAMAP	MF_03002. eIF3c.
InterPro	IPR008905. eIF3c_N. IPR000717. PCI_dom. [Graphical view]
Pfam	PF05470. eIF-3c_N. 2 hits. PF01399. PCI. 1 hit. [Graphical view]
SMART	SM00088. PINT. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	979121.

Entry information

Entry name

EIF3C_YEAST

Accession

Primary (citable) accession number: P32497
Secondary accession number(s): D6W0D6

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	October 1, 1996
Last modified:	April 3, 2013
This is version 119 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program