P24D4_ARATH
ID P24D4_ARATH Reviewed; 212 AA.
AC Q9FVU0;
DT 31-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Transmembrane emp24 domain-containing protein p24delta4;
DE AltName: Full=Protein CYTOPLASMIC BODIES;
DE AltName: Full=p24 family protein delta1b;
DE Short=p24delta1b;
DE AltName: Full=p24 family protein delta4;
DE Short=p24delta4;
DE Flags: Precursor;
GN Name=CYB; OrderedLocusNames=At1g57620; ORFNames=T8L23.9;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP DOMAIN, MUTAGENESIS OF 205-TYR-PHE-206 AND 209-LYS-LYS-210, SUBCELLULAR
RP LOCATION, AND SUBUNIT.
RX PubMed=15653796; DOI=10.1093/pcp/pch200;
RA Contreras I., Yang Y., Robinson D.G., Aniento F.;
RT "Sorting signals in the cytosolic tail of plant p24 proteins involved in
RT the interaction with the COPII coat.";
RL Plant Cell Physiol. 45:1779-1786(2004).
RN [7]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=22577184; DOI=10.1093/jxb/ers112;
RA Montesinos J.C., Sturm S., Langhans M., Hillmer S., Marcote M.J.,
RA Robinson D.G., Aniento F.;
RT "Coupled transport of Arabidopsis p24 proteins at the ER-Golgi interface.";
RL J. Exp. Bot. 63:4243-4261(2012).
RN [8]
RP GENE FAMILY, SUBCELLULAR LOCATION, AND COILED-COIL DOMAIN.
RX PubMed=22132757; DOI=10.1111/j.1600-0854.2011.01317.x;
RA Chen J., Qi X., Zheng H.;
RT "Subclass-specific localization and trafficking of Arabidopsis p24 proteins
RT in the ER-Golgi interface.";
RL Traffic 13:400-415(2012).
RN [9]
RP FUNCTION, MUTAGENESIS OF GLY-96, DISRUPTION PHENOTYPE, AND SUBCELLULAR
RP LOCATION.
RX PubMed=24330158; DOI=10.1111/tpj.12408;
RA Jancowski S., Catching A., Pighin J., Kudo T., Foissner I., Wasteneys G.O.;
RT "Trafficking of the myrosinase-associated protein GLL23 requires
RT NUC/MVP1/GOLD36/ERMO3 and the p24 protein CYB.";
RL Plant J. 77:497-510(2014).
CC -!- FUNCTION: Involved in vesicular protein trafficking. Mainly functions
CC in the early secretory pathway. Required for trafficking GLL23, a
CC component of the PYK10 complex. May act as a receptor facilitating its
CC packing into COPII carriers and export from the endoplasmic reticulum.
CC {ECO:0000269|PubMed:24330158}.
CC -!- SUBUNIT: Probably oligomerizes with other members of the EMP24/GP25L
CC family (By similarity). Associates with the COPI vesicle coat
CC (coatomer). Associates with the COPII vesicle coat (coatomer).
CC {ECO:0000250, ECO:0000269|PubMed:15653796}.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass type
CC I membrane protein. Golgi apparatus membrane; Single-pass type I
CC membrane protein. Note=Cycles between the endoplasmic reticulum and
CC Golgi via COPI and COPII dependent pathways. Mainly located in
CC endoplasmic reticulum.
CC -!- DOMAIN: The cytoplasmic C-terminal domain contains a functional
CC dilysine-retrieval motif, which is involved in the retrograde Golgi-to-
CC ER transport of the protein. {ECO:0000269|PubMed:15653796}.
CC -!- DISRUPTION PHENOTYPE: Formation of cytoplasmic bodies.
CC {ECO:0000269|PubMed:24330158}.
CC -!- SIMILARITY: Belongs to the EMP24/GP25L family. {ECO:0000305}.
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DR EMBL; AC079733; AAG50754.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE33445.1; -; Genomic_DNA.
DR EMBL; AK117498; BAC42161.1; -; mRNA.
DR EMBL; BT005172; AAO50705.1; -; mRNA.
DR EMBL; AY085744; AAM62962.1; -; mRNA.
DR PIR; D96610; D96610.
DR RefSeq; NP_176075.1; NM_104559.4.
DR AlphaFoldDB; Q9FVU0; -.
DR SMR; Q9FVU0; -.
DR BioGRID; 27363; 4.
DR IntAct; Q9FVU0; 1.
DR STRING; 3702.AT1G57620.1; -.
DR PaxDb; Q9FVU0; -.
DR PRIDE; Q9FVU0; -.
DR ProteomicsDB; 248784; -.
DR EnsemblPlants; AT1G57620.1; AT1G57620.1; AT1G57620.
DR GeneID; 842138; -.
DR Gramene; AT1G57620.1; AT1G57620.1; AT1G57620.
DR KEGG; ath:AT1G57620; -.
DR Araport; AT1G57620; -.
DR TAIR; locus:2206520; AT1G57620.
DR eggNOG; KOG1691; Eukaryota.
DR HOGENOM; CLU_066963_3_2_1; -.
DR InParanoid; Q9FVU0; -.
DR OMA; SPICEAV; -.
DR OrthoDB; 1294924at2759; -.
DR PhylomeDB; Q9FVU0; -.
DR PRO; PR:Q9FVU0; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9FVU0; baseline and differential.
DR Genevisible; Q9FVU0; AT.
DR GO; GO:0030134; C:COPII-coated ER to Golgi transport vesicle; IBA:GO_Central.
DR GO; GO:0005783; C:endoplasmic reticulum; IBA:GO_Central.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005793; C:endoplasmic reticulum-Golgi intermediate compartment; IBA:GO_Central.
DR GO; GO:0005794; C:Golgi apparatus; IBA:GO_Central.
DR GO; GO:0000139; C:Golgi membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0006888; P:endoplasmic reticulum to Golgi vesicle-mediated transport; IBA:GO_Central.
DR GO; GO:0007030; P:Golgi organization; IBA:GO_Central.
DR GO; GO:0006886; P:intracellular protein transport; IMP:TAIR.
DR InterPro; IPR015720; Emp24-like.
DR InterPro; IPR009038; GOLD_dom.
DR PANTHER; PTHR22811; PTHR22811; 1.
DR Pfam; PF01105; EMP24_GP25L; 1.
DR SMART; SM01190; EMP24_GP25L; 1.
DR PROSITE; PS50866; GOLD; 1.
PE 1: Evidence at protein level;
KW Coiled coil; Endoplasmic reticulum; ER-Golgi transport; Glycoprotein;
KW Golgi apparatus; Membrane; Methylation; Protein transport;
KW Reference proteome; Signal; Transmembrane; Transmembrane helix; Transport.
FT SIGNAL 1..25
FT /evidence="ECO:0000255"
FT CHAIN 26..212
FT /note="Transmembrane emp24 domain-containing protein
FT p24delta4"
FT /id="PRO_0000419784"
FT TOPO_DOM 26..179
FT /note="Lumenal"
FT /evidence="ECO:0000255"
FT TRANSMEM 180..200
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 201..212
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT DOMAIN 35..147
FT /note="GOLD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00096"
FT COILED 133..155
FT /evidence="ECO:0000255"
FT MOTIF 205..212
FT /note="COPI vesicle coat-binding"
FT MOTIF 205..206
FT /note="COPII vesicle coat-binding"
FT MOD_RES 165
FT /note="Omega-N-methylated arginine"
FT /evidence="ECO:0000250"
FT MOD_RES 170
FT /note="Omega-N-methylated arginine"
FT /evidence="ECO:0000250"
FT CARBOHYD 82
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT MUTAGEN 96
FT /note="G->E: In cyb-1; loss of trafficking between ER and
FT Golgi and formation of cytoplasmic bodies."
FT /evidence="ECO:0000269|PubMed:24330158"
FT MUTAGEN 205..206
FT /note="YF->AA: Disrupts association with COPII vesicle
FT coat. Slightly reduces association with COPI vesicle coat."
FT /evidence="ECO:0000269|PubMed:15653796"
FT MUTAGEN 209..210
FT /note="KK->SS: Disrupts association with COPI vesicle coat
FT but favors association with COPII vesicle coat."
FT /evidence="ECO:0000269|PubMed:15653796"
SQ SEQUENCE 212 AA; 23889 MW; E05AE85935F002BB CRC64;
MKKKMIPTTI LLSALIFSLS PICEAVWLTV PHTGSKCVSE EIQSNVIVLA DYLVISEEHS
IFPTVSVKVT APYGTVLHHR ENTTNGQFAF TTQESGTYLA CFEADAKSHG NKDFSINIDW
KTGIAAKDWD SIARKEKIEG VELEFKKLEG AVEAIHENLI YLRNREAEMR IVSEKTNSRV
AWYSIMSLGI CIVVSGLQIL YLKQYFEKKK LI
