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P53011

- SEH1_YEAST

UniProt

P53011 - SEH1_YEAST

Protein

Nucleoporin SEH1

Gene

SEH1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 135 (01 Oct 2014)
      Sequence version 1 (01 Oct 1996)
      Previous versions | rss
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    Functioni

    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. Involved in nuclear poly(A)+ RNA export and NPC biogenesis. It is also required for normal nuclear morphology. Component of the SEA complex which coats the vacuolar membrane and is involved in intracellular trafficking, autophagy, response to nitrogen starvation, and amino acid biogenesis.4 Publications

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. structural constituent of nuclear pore Source: SGD

    GO - Biological processi

    1. mRNA transport Source: UniProtKB-KW
    2. nucleocytoplasmic transport Source: SGD
    3. protein transport Source: UniProtKB-KW

    Keywords - Biological processi

    mRNA transport, Protein transport, Translocation, Transport

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30600-MONOMER.

    Protein family/group databases

    TCDBi1.I.1.1.1. the nuclear pore complex (npc) family.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nucleoporin SEH1
    Alternative name(s):
    Nuclear pore protein SEH1
    SEC13 homolog 1
    Gene namesi
    Name:SEH1
    Ordered Locus Names:YGL100W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VII

    Organism-specific databases

    CYGDiYGL100w.
    SGDiS000003068. SEH1.

    Subcellular locationi

    Nucleusnuclear pore complex 1 Publication. Cell membrane 1 Publication; Peripheral membrane protein 1 Publication; Cytoplasmic side 1 Publication. Vacuole membrane 1 Publication; Peripheral membrane protein 1 Publication. Cell membrane 1 Publication; Peripheral membrane protein 1 Publication; Nucleoplasmic side 1 Publication
    Note: Symmetric distribution.

    GO - Cellular componenti

    1. fungal-type vacuole membrane Source: SGD
    2. nuclear pore Source: SGD
    3. nuclear pore outer ring Source: SGD
    4. plasma membrane Source: UniProtKB-SubCell
    5. Seh1-associated complex Source: SGD

    Keywords - Cellular componenti

    Cell membrane, Membrane, Nuclear pore complex, Nucleus, Vacuole

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 349349Nucleoporin SEH1PRO_0000051215Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei257 – 2571Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP53011.
    PaxDbiP53011.
    PeptideAtlasiP53011.

    Expressioni

    Gene expression databases

    GenevestigatoriP53011.

    Interactioni

    Subunit structurei

    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. SEH1 is part of the heptameric 0.5 MDa autoassembling NUP84 NPC subcomplex (NUP84, NUP85, NUP120, NUP133, NUP145C, SEC13 and SEH1). Component of the SEA complex composed of at least IML1/SEA1, RTC1/SEA2, MTC5/SEA3, NPR2, NPR3, SEA4, SEC13 and SEH1.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    NUP85P466733EBI-16940,EBI-12345

    Protein-protein interaction databases

    BioGridi33149. 213 interactions.
    DIPiDIP-4193N.
    IntActiP53011. 21 interactions.
    MINTiMINT-547303.
    STRINGi4932.YGL100W.

    Structurei

    Secondary structure

    1
    349
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi12 – 176
    Beta strandi19 – 2810
    Beta strandi31 – 388
    Beta strandi40 – 423
    Beta strandi45 – 528
    Beta strandi58 – 636
    Helixi66 – 683
    Beta strandi70 – 767
    Beta strandi77 – 793
    Beta strandi81 – 866
    Beta strandi97 – 1048
    Beta strandi111 – 1166
    Helixi119 – 1213
    Beta strandi123 – 1297
    Beta strandi133 – 1386
    Beta strandi149 – 1568
    Beta strandi169 – 1735
    Beta strandi177 – 1793
    Beta strandi182 – 1876
    Beta strandi190 – 1967
    Beta strandi202 – 2076
    Beta strandi215 – 2206
    Beta strandi227 – 2359
    Beta strandi240 – 2478
    Beta strandi291 – 30010
    Beta strandi307 – 3126
    Beta strandi314 – 3163
    Beta strandi319 – 3235
    Beta strandi328 – 3336
    Beta strandi339 – 3457

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3EWEX-ray3.50A/C1-349[»]
    3F3FX-ray2.90A/B/E/F1-349[»]
    3F3GX-ray3.75A/B/E/F1-349[»]
    3F3PX-ray3.20A/B/E/F/I/J1-349[»]
    ProteinModelPortaliP53011.
    SMRiP53011. Positions 1-349.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP53011.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati7 – 4640WD 1Add
    BLAST
    Repeati53 – 9442WD 2Add
    BLAST
    Repeati106 – 14742WD 3Add
    BLAST
    Repeati153 – 19240WD 4Add
    BLAST
    Repeati210 – 25344WD 5Add
    BLAST
    Repeati302 – 34140WD 6Add
    BLAST

    Sequence similaritiesi

    Belongs to the WD repeat SEC13 family.Curated
    Contains 6 WD repeats.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat, WD repeat

    Phylogenomic databases

    eggNOGiCOG2319.
    GeneTreeiENSGT00550000074999.
    HOGENOMiHOG000216896.
    KOiK14299.
    OMAiYEAPDIM.
    OrthoDBiEOG7TQVBP.

    Family and domain databases

    Gene3Di2.130.10.10. 3 hits.
    InterProiIPR015943. WD40/YVTN_repeat-like_dom.
    IPR001680. WD40_repeat.
    IPR017986. WD40_repeat_dom.
    [Graphical view]
    PfamiPF00400. WD40. 5 hits.
    [Graphical view]
    SMARTiSM00320. WD40. 5 hits.
    [Graphical view]
    SUPFAMiSSF50978. SSF50978. 2 hits.
    PROSITEiPS50082. WD_REPEATS_2. 3 hits.
    PS50294. WD_REPEATS_REGION. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P53011-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQPFDSGHDD LVHDVVYDFY GRHVATCSSD QHIKVFKLDK DTSNWELSDS    50
    WRAHDSSIVA IDWASPEYGR IIASASYDKT VKLWEEDPDQ EECSGRRWNK 100
    LCTLNDSKGS LYSVKFAPAH LGLKLACLGN DGILRLYDAL EPSDLRSWTL 150
    TSEMKVLSIP PANHLQSDFC LSWCPSRFSP EKLAVSALEQ AIIYQRGKDG 200
    KLHVAAKLPG HKSLIRSISW APSIGRWYQL IATGCKDGRI RIFKITEKLS 250
    PLASEESLTN SNMFDNSADV DMDAQGRSDS NTEEKAELQS NLQVELLSEH 300
    DDHNGEVWSV SWNLTGTILS SAGDDGKVRL WKATYSNEFK CMSVITAQQ 349
    Length:349
    Mass (Da):39,123
    Last modified:October 1, 1996 - v1
    Checksum:iEAF75B9DE074106B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X90994 Genomic DNA. Translation: CAA62480.1.
    Z72622 Genomic DNA. Translation: CAA96806.1.
    AY558497 Genomic DNA. Translation: AAS56823.1.
    BK006941 Genomic DNA. Translation: DAA08006.1.
    PIRiS62137.
    RefSeqiNP_011415.1. NM_001180965.1.

    Genome annotation databases

    EnsemblFungiiYGL100W; YGL100W; YGL100W.
    GeneIDi852778.
    KEGGisce:YGL100W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X90994 Genomic DNA. Translation: CAA62480.1 .
    Z72622 Genomic DNA. Translation: CAA96806.1 .
    AY558497 Genomic DNA. Translation: AAS56823.1 .
    BK006941 Genomic DNA. Translation: DAA08006.1 .
    PIRi S62137.
    RefSeqi NP_011415.1. NM_001180965.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3EWE X-ray 3.50 A/C 1-349 [» ]
    3F3F X-ray 2.90 A/B/E/F 1-349 [» ]
    3F3G X-ray 3.75 A/B/E/F 1-349 [» ]
    3F3P X-ray 3.20 A/B/E/F/I/J 1-349 [» ]
    ProteinModelPortali P53011.
    SMRi P53011. Positions 1-349.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33149. 213 interactions.
    DIPi DIP-4193N.
    IntActi P53011. 21 interactions.
    MINTi MINT-547303.
    STRINGi 4932.YGL100W.

    Protein family/group databases

    TCDBi 1.I.1.1.1. the nuclear pore complex (npc) family.

    Proteomic databases

    MaxQBi P53011.
    PaxDbi P53011.
    PeptideAtlasi P53011.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YGL100W ; YGL100W ; YGL100W .
    GeneIDi 852778.
    KEGGi sce:YGL100W.

    Organism-specific databases

    CYGDi YGL100w.
    SGDi S000003068. SEH1.

    Phylogenomic databases

    eggNOGi COG2319.
    GeneTreei ENSGT00550000074999.
    HOGENOMi HOG000216896.
    KOi K14299.
    OMAi YEAPDIM.
    OrthoDBi EOG7TQVBP.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30600-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P53011.
    NextBioi 972254.
    PROi P53011.

    Gene expression databases

    Genevestigatori P53011.

    Family and domain databases

    Gene3Di 2.130.10.10. 3 hits.
    InterProi IPR015943. WD40/YVTN_repeat-like_dom.
    IPR001680. WD40_repeat.
    IPR017986. WD40_repeat_dom.
    [Graphical view ]
    Pfami PF00400. WD40. 5 hits.
    [Graphical view ]
    SMARTi SM00320. WD40. 5 hits.
    [Graphical view ]
    SUPFAMi SSF50978. SSF50978. 2 hits.
    PROSITEi PS50082. WD_REPEATS_2. 3 hits.
    PS50294. WD_REPEATS_REGION. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A novel complex of nucleoporins, which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores."
      Siniossoglou S., Wimmer C., Rieger M., Doye V., Tekotte H., Weise C., Emig S., Segref A., Hurt E.C.
      Cell 84:265-275(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 116-121 AND 136-146, FUNCTION IN NUCLEAR MRNA EXPORT.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
      Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
      , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
      Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. "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] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION, NPC SUBUNIT LOCATION.
    6. "Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins."
      Lutzmann M., Kunze R., Buerer A., Aebi U., Hurt E.C.
      EMBO J. 21:387-397(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, NUP84 NPC SUBCOMPLEX ASSEMBLY/STRUCTURE.
    7. "Genome-wide nuclear morphology screen identifies novel genes involved in nuclear architecture and gene-silencing in Saccharomyces cerevisiae."
      Teixeira M.T., Dujon B., Fabre E.
      J. Mol. Biol. 321:551-561(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, NUCLEAR MORPHOLOGY.
    8. "Peering through the pore: nuclear pore complex structure, assembly, and function."
      Suntharalingam M., Wente S.R.
      Dev. Cell 4:775-789(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    10. "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-257, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. "A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae."
      Dokudovskaya S., Waharte F., Schlessinger A., Pieper U., Devos D.P., Cristea I.M., Williams R., Salamero J., Chait B.T., Sali A., Field M.C., Rout M.P., Dargemont C.
      Mol. Cell. Proteomics 10:M110.006478.1-M110.006478.17(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, IDENTIFICATION IN THE SEA COMPLEX, FUNCTION.

    Entry informationi

    Entry nameiSEH1_YEAST
    AccessioniPrimary (citable) accession number: P53011
    Secondary accession number(s): D6VU45
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 135 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 952 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome VII
      Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

    External Data

    Dasty 3