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O94855

- SC24D_HUMAN

UniProt

O94855 - SC24D_HUMAN

Protein

Protein transport protein Sec24D

Gene

SEC24D

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 123 (01 Oct 2014)
      Sequence version 2 (25 Nov 2008)
      Previous versions | rss
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    Functioni

    Component of the COPII coat, that covers ER-derived vesicles involved in transport from the endoplasmic reticulum to the Golgi apparatus. COPII acts in the cytoplasm to promote the transport of secretory, plasma membrane, and vacuolar proteins from the endoplasmic reticulum to the Golgi complex.

    GO - Molecular functioni

    1. zinc ion binding Source: InterPro

    GO - Biological processi

    1. antigen processing and presentation of exogenous peptide antigen via MHC class II Source: Reactome
    2. antigen processing and presentation of peptide antigen via MHC class I Source: Reactome
    3. cellular protein metabolic process Source: Reactome
    4. COPII vesicle coating Source: Reactome
    5. ER to Golgi vesicle-mediated transport Source: UniProtKB
    6. intracellular protein transport Source: InterPro
    7. membrane organization Source: Reactome
    8. post-translational protein modification Source: Reactome
    9. protein N-linked glycosylation via asparagine Source: Reactome
    10. small molecule metabolic process Source: Reactome

    Keywords - Biological processi

    ER-Golgi transport, Protein transport, Transport

    Enzyme and pathway databases

    ReactomeiREACT_121399. MHC class II antigen presentation.
    REACT_12507. COPII (Coat Protein 2) Mediated Vesicle Transport.
    REACT_147797. Regulation of cholesterol biosynthesis by SREBP (SREBF).
    REACT_75795. Antigen Presentation: Folding, assembly and peptide loading of class I MHC.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein transport protein Sec24D
    Alternative name(s):
    SEC24-related protein D
    Gene namesi
    Name:SEC24D
    Synonyms:KIAA0755
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 4

    Organism-specific databases

    HGNCiHGNC:10706. SEC24D.

    Subcellular locationi

    Cytoplasm By similarity. Cytoplasmperinuclear region By similarity. Endoplasmic reticulum membrane By similarity. Golgi apparatus membrane By similarity

    GO - Cellular componenti

    1. COPII vesicle coat Source: UniProtKB
    2. cytosol Source: Reactome
    3. endoplasmic reticulum membrane Source: Reactome
    4. ER to Golgi transport vesicle membrane Source: Reactome
    5. Golgi membrane Source: UniProtKB-SubCell
    6. perinuclear region of cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Endoplasmic reticulum, Golgi apparatus, Membrane

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA35629.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 10321032Protein transport protein Sec24DPRO_0000205157Add
    BLAST

    Proteomic databases

    MaxQBiO94855.
    PaxDbiO94855.
    PRIDEiO94855.

    PTM databases

    PhosphoSiteiO94855.

    Expressioni

    Tissue specificityi

    Ubiquitously expressed, with higher amounts in placenta, pancreas, heart and liver.

    Gene expression databases

    ArrayExpressiO94855.
    BgeeiO94855.
    CleanExiHS_SEC24D.
    GenevestigatoriO94855.

    Organism-specific databases

    HPAiHPA041626.

    Interactioni

    Subunit structurei

    COPII is composed of at least five proteins: the Sec23/24 complex, the Sec13/31 complex and Sar1. Interacts with TMED2 and TMED10.1 Publication

    Protein-protein interaction databases

    BioGridi115204. 17 interactions.
    IntActiO94855. 9 interactions.
    MINTiMINT-1184580.
    STRINGi9606.ENSP00000280551.

    Structurei

    Secondary structure

    1
    1032
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi267 – 27812
    Beta strandi281 – 2844
    Beta strandi287 – 2893
    Beta strandi300 – 3023
    Beta strandi304 – 3063
    Turni309 – 3113
    Beta strandi312 – 32211
    Helixi323 – 3297
    Beta strandi334 – 3374
    Turni356 – 3583
    Turni364 – 3663
    Beta strandi375 – 3773
    Helixi378 – 3803
    Beta strandi382 – 3843
    Turni386 – 3883
    Beta strandi391 – 3933
    Helixi396 – 3983
    Beta strandi404 – 4063
    Turni408 – 4103
    Helixi411 – 4133
    Helixi415 – 4184
    Beta strandi420 – 4256
    Helixi428 – 4303
    Helixi432 – 4343
    Beta strandi441 – 4477
    Helixi450 – 4545
    Helixi457 – 46812
    Helixi469 – 4713
    Beta strandi478 – 4803
    Beta strandi484 – 49815
    Beta strandi507 – 5115
    Beta strandi522 – 5276
    Turni529 – 5324
    Helixi533 – 54816
    Helixi558 – 57114
    Beta strandi575 – 5817
    Beta strandi587 – 5893
    Helixi607 – 6115
    Beta strandi614 – 6163
    Helixi617 – 62711
    Beta strandi630 – 6367
    Helixi644 – 6474
    Helixi649 – 6535
    Beta strandi658 – 6603
    Helixi666 – 68217
    Beta strandi685 – 69511
    Beta strandi699 – 7079
    Beta strandi711 – 7144
    Beta strandi716 – 7249
    Beta strandi727 – 7359
    Turni739 – 7413
    Beta strandi742 – 75211
    Beta strandi758 – 77114
    Helixi773 – 7786
    Helixi782 – 79615
    Turni797 – 7993
    Helixi802 – 82322
    Beta strandi832 – 8354
    Helixi837 – 8393
    Helixi842 – 85110
    Helixi853 – 8553
    Beta strandi858 – 8614
    Helixi863 – 87513
    Helixi878 – 8858
    Beta strandi888 – 8914
    Beta strandi897 – 8993
    Helixi910 – 9123
    Beta strandi918 – 9225
    Beta strandi924 – 9318
    Helixi937 – 9448
    Beta strandi945 – 9484
    Helixi949 – 9513
    Helixi966 – 97813
    Beta strandi986 – 9927
    Helixi998 – 10014
    Helixi1016 – 102914

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3EFOX-ray2.70B266-1032[»]
    3EG9X-ray3.00B266-1032[»]
    ProteinModelPortaliO94855.
    SMRiO94855. Positions 263-1032.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO94855.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni363 – 38826Zinc finger-likeAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi10 – 293284Pro-richAdd
    BLAST

    Sequence similaritiesi

    Belongs to the SEC23/SEC24 family. SEC24 subfamily.Curated

    Phylogenomic databases

    eggNOGiCOG5028.
    HOGENOMiHOG000196365.
    HOVERGENiHBG062229.
    KOiK14007.
    OMAiPMGGQSM.
    OrthoDBiEOG700877.
    PhylomeDBiO94855.
    TreeFamiTF300464.

    Family and domain databases

    Gene3Di3.40.20.10. 1 hit.
    3.40.50.410. 1 hit.
    InterProiIPR029006. ADF-H/Gelsolin-like_dom.
    IPR007123. Gelsolin-like_dom.
    IPR006900. Sec23/24_helical_dom.
    IPR006896. Sec23/24_trunk_dom.
    IPR012990. Sec23_24_beta_S.
    IPR002035. VWF_A.
    IPR006895. Znf_Sec23_Sec24.
    [Graphical view]
    PfamiPF00626. Gelsolin. 1 hit.
    PF08033. Sec23_BS. 1 hit.
    PF04815. Sec23_helical. 1 hit.
    PF04811. Sec23_trunk. 1 hit.
    PF04810. zf-Sec23_Sec24. 1 hit.
    [Graphical view]
    SUPFAMiSSF53300. SSF53300. 1 hit.
    SSF81811. SSF81811. 1 hit.

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: O94855-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MSQQGYVATP PYSQPQPGIG LSPPHYGHYG DPSHTASPTG MMKPAGPLGA     50
    TATRGMLPPG PPPPGPHQFG QNGAHATGHP PQRFPGPPPV NNVASSHAPY 100
    QPSAQSSYPG PISTSSVTQL GSQLSAMQIN SYGSGMAPPS QGPPGPLSAT 150
    SLQTPPRPPQ PSILQPGSQV LPPPPTTLNG PGASPLPLPM YRPDGLSGPP 200
    PPNAQYQPPP LPGQTLGAGY PPQQANSGPQ MAGAQLSYPG GFPGGPAQMA 250
    GPPQPQKKLD PDSIPSPIQV IENDRASRGG QVYATNTRGQ IPPLVTTDCM 300
    IQDQGNASPR FIRCTTYCFP CTSDMAKQAQ IPLAAVIKPF ATIPSNESPL 350
    YLVNHGESGP VRCNRCKAYM CPFMQFIEGG RRYQCGFCNC VNDVPPFYFQ 400
    HLDHIGRRLD HYEKPELSLG SYEYVATLDY CRKSKPPNPP AFIFMIDVSY 450
    SNIKNGLVKL ICEELKTMLE KIPKEEQEET SAIRVGFITY NKVLHFFNVK 500
    SNLAQPQMMV VTDVGEVFVP LLDGFLVNYQ ESQSVIHNLL DQIPDMFADS 550
    NENETVFAPV IQAGMEALKA ADCPGKLFIF HSSLPTAEAP GKLKNRDDKK 600
    LVNTDKEKIL FQPQTNVYDS LAKDCVAHGC SVTLFLFPSQ YVDVASLGLV 650
    PQLTGGTLYK YNNFQMHLDR QQFLNDLRND IEKKIGFDAI MRVRTSTGFR 700
    ATDFFGGILM NNTTDVEMAA IDCDKAVTVE FKHDDKLSED SGALIQCAVL 750
    YTTISGQRRL RIHNLGLNCS SQLADLYKSC ETDALINFFA KSAFKAVLHQ 800
    PLKVIREILV NQTAHMLACY RKNCASPSAA SQLILPDSMK VLPVYMNCLL 850
    KNCVLLSRPE ISTDERAYQR QLVMTMGVAD SQLFFYPQLL PIHTLDVKST 900
    MLPAAVRCSE SRLSEEGIFL LANGLHMFLW LGVSSPPELI QGIFNVPSFA 950
    HINTDMTLLP EVGNPYSQQL RMIMGIIQQK RPYSMKLTIV KQREQPEMVF 1000
    RQFLVEDKGL YGGSSYVDFL CCVHKEICQL LN 1032
    Length:1,032
    Mass (Da):113,010
    Last modified:November 25, 2008 - v2
    Checksum:iB46E566F096F37F0
    GO
    Isoform 2 (identifier: O94855-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         224-224: Q → QA

    Note: No experimental confirmation available.

    Show »
    Length:1,033
    Mass (Da):113,081
    Checksum:i4DBA3D9F630F0043
    GO

    Sequence cautioni

    The sequence BAA34475.2 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti559 – 5591P → S in AAD28756. (PubMed:10329445)Curated
    Sequence conflicti559 – 5591P → S in BAA34475. (PubMed:9872452)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti42 – 421M → T.
    Corresponds to variant rs10029206 [ dbSNP | Ensembl ].
    VAR_047472
    Natural varianti193 – 1931P → L.
    Corresponds to variant rs6844109 [ dbSNP | Ensembl ].
    VAR_047473
    Natural varianti496 – 4961F → I.
    Corresponds to variant rs11723368 [ dbSNP | Ensembl ].
    VAR_047474

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei224 – 2241Q → QA in isoform 2. 1 PublicationVSP_035761

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF130464 mRNA. Translation: AAD28756.2.
    AB018298 mRNA. Translation: BAA34475.2. Different initiation.
    CH471229 Genomic DNA. Translation: EAW73656.1.
    BC035761 mRNA. Translation: AAH35761.1.
    CCDSiCCDS3710.1. [O94855-1]
    RefSeqiNP_055637.2. NM_014822.2. [O94855-1]
    XP_005263435.1. XM_005263378.1. [O94855-2]
    XP_005263436.1. XM_005263379.1. [O94855-2]
    UniGeneiHs.189641.

    Genome annotation databases

    EnsembliENST00000280551; ENSP00000280551; ENSG00000150961. [O94855-1]
    GeneIDi9871.
    KEGGihsa:9871.
    UCSCiuc003ici.4. human. [O94855-1]
    uc003icj.4. human. [O94855-2]

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF130464 mRNA. Translation: AAD28756.2 .
    AB018298 mRNA. Translation: BAA34475.2 . Different initiation.
    CH471229 Genomic DNA. Translation: EAW73656.1 .
    BC035761 mRNA. Translation: AAH35761.1 .
    CCDSi CCDS3710.1. [O94855-1 ]
    RefSeqi NP_055637.2. NM_014822.2. [O94855-1 ]
    XP_005263435.1. XM_005263378.1. [O94855-2 ]
    XP_005263436.1. XM_005263379.1. [O94855-2 ]
    UniGenei Hs.189641.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3EFO X-ray 2.70 B 266-1032 [» ]
    3EG9 X-ray 3.00 B 266-1032 [» ]
    ProteinModelPortali O94855.
    SMRi O94855. Positions 263-1032.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 115204. 17 interactions.
    IntActi O94855. 9 interactions.
    MINTi MINT-1184580.
    STRINGi 9606.ENSP00000280551.

    PTM databases

    PhosphoSitei O94855.

    Proteomic databases

    MaxQBi O94855.
    PaxDbi O94855.
    PRIDEi O94855.

    Protocols and materials databases

    DNASUi 9871.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000280551 ; ENSP00000280551 ; ENSG00000150961 . [O94855-1 ]
    GeneIDi 9871.
    KEGGi hsa:9871.
    UCSCi uc003ici.4. human. [O94855-1 ]
    uc003icj.4. human. [O94855-2 ]

    Organism-specific databases

    CTDi 9871.
    GeneCardsi GC04M119643.
    H-InvDB HIX0004459.
    HGNCi HGNC:10706. SEC24D.
    HPAi HPA041626.
    MIMi 607186. gene.
    neXtProti NX_O94855.
    PharmGKBi PA35629.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG5028.
    HOGENOMi HOG000196365.
    HOVERGENi HBG062229.
    KOi K14007.
    OMAi PMGGQSM.
    OrthoDBi EOG700877.
    PhylomeDBi O94855.
    TreeFami TF300464.

    Enzyme and pathway databases

    Reactomei REACT_121399. MHC class II antigen presentation.
    REACT_12507. COPII (Coat Protein 2) Mediated Vesicle Transport.
    REACT_147797. Regulation of cholesterol biosynthesis by SREBP (SREBF).
    REACT_75795. Antigen Presentation: Folding, assembly and peptide loading of class I MHC.

    Miscellaneous databases

    ChiTaRSi SEC24D. human.
    EvolutionaryTracei O94855.
    GeneWikii SEC24D.
    GenomeRNAii 9871.
    NextBioi 37211.
    PROi O94855.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O94855.
    Bgeei O94855.
    CleanExi HS_SEC24D.
    Genevestigatori O94855.

    Family and domain databases

    Gene3Di 3.40.20.10. 1 hit.
    3.40.50.410. 1 hit.
    InterProi IPR029006. ADF-H/Gelsolin-like_dom.
    IPR007123. Gelsolin-like_dom.
    IPR006900. Sec23/24_helical_dom.
    IPR006896. Sec23/24_trunk_dom.
    IPR012990. Sec23_24_beta_S.
    IPR002035. VWF_A.
    IPR006895. Znf_Sec23_Sec24.
    [Graphical view ]
    Pfami PF00626. Gelsolin. 1 hit.
    PF08033. Sec23_BS. 1 hit.
    PF04815. Sec23_helical. 1 hit.
    PF04811. Sec23_trunk. 1 hit.
    PF04810. zf-Sec23_Sec24. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53300. SSF53300. 1 hit.
    SSF81811. SSF81811. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Tissue: Pancreas.
    2. "Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
      Nagase T., Ishikawa K., Suyama M., Kikuno R., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
      DNA Res. 5:277-286(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Brain.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Tissue: Lymph.
    5. "Selective export of human GPI-anchored proteins from the endoplasmic reticulum."
      Bonnon C., Wendeler M.W., Paccaud J.P., Hauri H.P.
      J. Cell Sci. 123:1705-1715(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH TMED2 AND TMED10.
    6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiSC24D_HUMAN
    AccessioniPrimary (citable) accession number: O94855
    Secondary accession number(s): Q8IYI7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 21, 2001
    Last sequence update: November 25, 2008
    Last modified: October 1, 2014
    This is version 123 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 4
      Human chromosome 4: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3