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Protein

Eukaryotic translation initiation factor 3 subunit C

Gene

NIP1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation.UniRule annotation1 Publication

GO - Molecular functioni

  • translation initiation factor activity Source: SGD
  • translation initiation factor binding Source: SGD

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Initiation factor

Keywords - Biological processi

Protein biosynthesis

Enzyme and pathway databases

BioCyciYEAST:G3O-32973-MONOMER.
ReactomeiR-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-72695. Formation of the ternary complex, and subsequently, the 43S complex.
R-SCE-72702. Ribosomal scanning and start codon recognition.

Names & Taxonomyi

Protein namesi
Recommended name:
Eukaryotic translation initiation factor 3 subunit CUniRule annotation
Short name:
eIF3cUniRule annotation
Alternative name(s):
Eukaryotic translation initiation factor 3 93 kDa subunit
Short name:
eIF3 p93UniRule annotation
Nuclear transport protein NIP1
Translation initiation factor eIF3, p93 subunit
Gene namesi
Name:NIP1UniRule annotation
Ordered Locus Names:YMR309C
ORF Names:YM9924.01C, YM9952.11C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YMR309C.
SGDiS000004926. NIP1.

Subcellular locationi

  • Cytoplasm UniRule annotation1 Publication

  • Note: Mainly cytoplasmic.

GO - Cellular componenti

  • cytoplasm Source: SGD
  • cytoplasmic stress granule Source: SGD
  • eukaryotic 43S preinitiation complex Source: UniProtKB-HAMAP
  • eukaryotic 48S preinitiation complex Source: UniProtKB-HAMAP
  • eukaryotic translation initiation factor 3 complex Source: SGD
  • multi-eIF complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001235301 – 812Eukaryotic translation initiation factor 3 subunit CAdd BLAST812

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei98PhosphoserineCombined sources1
Modified residuei99PhosphoserineCombined sources1
Modified residuei103PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP32497.
PRIDEiP32497.

PTM databases

iPTMnetiP32497.

Interactioni

Subunit structurei

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 SUI1.7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PRT1P061039EBI-8965,EBI-8973
RPB4P204335EBI-8965,EBI-15777
RPG1P3824911EBI-8965,EBI-8981
TIF5P384315EBI-8965,EBI-9038

GO - Molecular functioni

  • translation initiation factor binding Source: SGD

Protein-protein interaction databases

BioGridi35489. 87 interactors.
DIPiDIP-1470N.
IntActiP32497. 59 interactors.
MINTiMINT-388745.

Structurei

Secondary structure

1812
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi252 – 265Combined sources14
Beta strandi267 – 269Combined sources3
Helixi272 – 285Combined sources14
Helixi289 – 306Combined sources18
Turni307 – 309Combined sources3
Beta strandi310 – 312Combined sources3
Helixi315 – 335Combined sources21
Helixi338 – 340Combined sources3
Turni342 – 344Combined sources3
Turni350 – 355Combined sources6
Turni363 – 366Combined sources4
Helixi368 – 386Combined sources19
Helixi392 – 418Combined sources27
Helixi422 – 438Combined sources17
Turni439 – 442Combined sources4
Helixi445 – 457Combined sources13
Helixi469 – 472Combined sources4
Helixi478 – 489Combined sources12
Turni490 – 492Combined sources3
Helixi496 – 513Combined sources18
Helixi516 – 526Combined sources11
Helixi530 – 534Combined sources5
Helixi538 – 556Combined sources19
Helixi560 – 571Combined sources12
Helixi576 – 579Combined sources4
Helixi585 – 592Combined sources8
Helixi595 – 602Combined sources8
Helixi608 – 610Combined sources3
Helixi614 – 637Combined sources24
Helixi652 – 660Combined sources9
Helixi671 – 684Combined sources14
Helixi687 – 695Combined sources9
Helixi698 – 702Combined sources5
Helixi706 – 729Combined sources24
Turni730 – 732Combined sources3
Beta strandi733 – 737Combined sources5
Helixi738 – 745Combined sources8
Helixi749 – 763Combined sources15
Beta strandi768 – 770Combined sources3
Turni771 – 774Combined sources4
Beta strandi775 – 777Combined sources3
Helixi784 – 793Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JAPelectron microscopy4.90p193-812[»]
4U1CX-ray3.50C247-812[»]
ProteinModelPortaliP32497.
SMRiP32497.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini650 – 780PCIUniRule annotationAdd BLAST131

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi15 – 147Asp/Glu-rich (acidic)Add BLAST133
Compositional biasi15 – 36Ser-richAdd BLAST22

Sequence similaritiesi

Belongs to the eIF-3 subunit C family.UniRule annotation
Contains 1 PCI domain.UniRule annotation

Phylogenomic databases

GeneTreeiENSGT00390000017900.
HOGENOMiHOG000029414.
InParanoidiP32497.
KOiK03252.
OMAiDEHAEME.
OrthoDBiEOG092C17F5.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
HAMAPiMF_03002. eIF3c. 1 hit.
InterProiIPR027516. EIF3C.
IPR008905. EIF3C_N_dom.
IPR000717. PCI_dom.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF05470. eIF-3c_N. 2 hits.
PF01399. PCI. 1 hit.
[Graphical view]
SMARTiSM00088. PINT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P32497-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRFFSSNYE YDVASSSSEE DLLSSSEEDL LSSSSSESEL DQESDDSFFN
60 70 80 90 100
ESESESEADV DSDDSDAKPY GPDWFKKSEF RKQGGGSNKF LKSSNYDSSD
110 120 130 140 150
EESDEEDGKK VVKSAKEKLL DEMQDVYNKI SQAENSDDWL TISNEFDLIS
160 170 180 190 200
RLLVRAQQQN WGTPNIFIKV VAQVEDAVNN TQQADLKNKA VARAYNTTKQ
210 220 230 240 250
RVKKVSRENE DSMAKFRNDP ESFDKEPTAD LDISANGFTI SSSQGNDQAV
260 270 280 290 300
QEDFFTRLQT IIDSRGKKTV NQQSLISTLE ELLTVAEKPY EFIMAYLTLI
310 320 330 340 350
PSRFDASANL SYQPIDQWKS SFNDISKLLS ILDQTIDTYQ VNEFADPIDF
360 370 380 390 400
IEDEPKEDSD GVKRILGSIF SFVERLDDEF MKSLLNIDPH SSDYLIRLRD
410 420 430 440 450
EQSIYNLILR TQLYFEATLK DEHDLERALT RPFVKRLDHI YYKSENLIKI
460 470 480 490 500
METAAWNIIP AQFKSKFTSK DQLDSADYVD NLIDGLSTIL SKQNNIAVQK
510 520 530 540 550
RAILYNIYYT ALNKDFQTAK DMLLTSQVQT NINQFDSSLQ ILFNRVVVQL
560 570 580 590 600
GLSAFKLCLI EECHQILNDL LSSSHLREIL GQQSLHRISL NSSNNASADE
610 620 630 640 650
RARQCLPYHQ HINLDLIDVV FLTCSLLIEI PRMTAFYSGI KVKRIPYSPK
660 670 680 690 700
SIRRSLEHYD KLSFQGPPET LRDYVLFAAK SMQKGNWRDS VKYLREIKSW
710 720 730 740 750
ALLPNMETVL NSLTERVQVE SLKTYFFSFK RFYSSFSVAK LAELFDLPEN
760 770 780 790 800
KVVEVLQSVI AELEIPAKLN DEKTIFVVEK GDEITKLEEA MVKLNKEYKI
810
AKERLNPPSN RR
Length:812
Mass (Da):93,204
Last modified:October 1, 1996 - v2
Checksum:iEE05097C44C45A4C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti111V → D in L02899 (PubMed:1332047).Curated1
Sequence conflicti583Q → H in L02899 (PubMed:1332047).Curated1
Sequence conflicti641K → N in L02899 (PubMed:1332047).Curated1
Sequence conflicti643K → N in L02899 (PubMed:1332047).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L02899 Genomic DNA. No translation available.
Z54141 Genomic DNA. Translation: CAA90827.1.
Z49212 Genomic DNA. Translation: CAA89142.1.
BK006946 Genomic DNA. Translation: DAA10210.1.
PIRiA46417.
RefSeqiNP_014040.1. NM_001182820.1.

Genome annotation databases

EnsemblFungiiYMR309C; YMR309C; YMR309C.
GeneIDi855357.
KEGGisce:YMR309C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L02899 Genomic DNA. No translation available.
Z54141 Genomic DNA. Translation: CAA90827.1.
Z49212 Genomic DNA. Translation: CAA89142.1.
BK006946 Genomic DNA. Translation: DAA10210.1.
PIRiA46417.
RefSeqiNP_014040.1. NM_001182820.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JAPelectron microscopy4.90p193-812[»]
4U1CX-ray3.50C247-812[»]
ProteinModelPortaliP32497.
SMRiP32497.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35489. 87 interactors.
DIPiDIP-1470N.
IntActiP32497. 59 interactors.
MINTiMINT-388745.

PTM databases

iPTMnetiP32497.

Proteomic databases

MaxQBiP32497.
PRIDEiP32497.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYMR309C; YMR309C; YMR309C.
GeneIDi855357.
KEGGisce:YMR309C.

Organism-specific databases

EuPathDBiFungiDB:YMR309C.
SGDiS000004926. NIP1.

Phylogenomic databases

GeneTreeiENSGT00390000017900.
HOGENOMiHOG000029414.
InParanoidiP32497.
KOiK03252.
OMAiDEHAEME.
OrthoDBiEOG092C17F5.

Enzyme and pathway databases

BioCyciYEAST:G3O-32973-MONOMER.
ReactomeiR-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-72695. Formation of the ternary complex, and subsequently, the 43S complex.
R-SCE-72702. Ribosomal scanning and start codon recognition.

Miscellaneous databases

PROiP32497.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
HAMAPiMF_03002. eIF3c. 1 hit.
InterProiIPR027516. EIF3C.
IPR008905. EIF3C_N_dom.
IPR000717. PCI_dom.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF05470. eIF-3c_N. 2 hits.
PF01399. PCI. 1 hit.
[Graphical view]
SMARTiSM00088. PINT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiEIF3C_YEAST
AccessioniPrimary (citable) accession number: P32497
Secondary accession number(s): D6W0D6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1996
Last modified: November 30, 2016
This is version 153 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 78900 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Translation initiation factors
    List of translation initiation factor entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.