C1D_HUMAN
ID C1D_HUMAN Reviewed; 141 AA.
AC Q13901; A8K336; D6W5F8; Q05D64;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 163.
DE RecName: Full=Nuclear nucleic acid-binding protein C1D;
DE Short=hC1D;
GN Name=C1D;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND SUBUNIT.
RC TISSUE=Term placenta;
RX PubMed=9469821; DOI=10.1093/nar/26.5.1160;
RA Nehls P., Keck T., Greferath R., Spiess E., Glaser T., Rothbarth K.,
RA Stammer H., Werner D.;
RT "cDNA cloning, recombinant expression and characterization of polypeptides
RT with exceptional DNA affinity.";
RL Nucleic Acids Res. 26:1160-1166(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15815621; DOI=10.1038/nature03466;
RA Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P.,
RA Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C.,
RA Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L.,
RA Du H., Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A.,
RA Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J.,
RA Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M.,
RA Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T.,
RA Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S.,
RA Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K.,
RA McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C.,
RA Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S.,
RA Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C.,
RA Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M.,
RA Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C.,
RA Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J.,
RA Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E.,
RA Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X.,
RA Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M.,
RA Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C.,
RA Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S.,
RA Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H.,
RA Wilson R.K.;
RT "Generation and annotation of the DNA sequences of human chromosomes 2 and
RT 4.";
RL Nature 434:724-731(2005).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Bone marrow, Lung, and Uterus;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [6]
RP FUNCTION, INDUCTION, PHOSPHORYLATION, AND INTERACTION WITH PRKDC.
RX PubMed=9679063; DOI=10.1101/gad.12.14.2188;
RA Yavuzer U., Smith G.C.M., Bliss T., Werner D., Jackson S.P.;
RT "DNA end-independent activation of DNA-PK mediated via association with the
RT DNA-binding protein C1D.";
RL Genes Dev. 12:2188-2199(1998).
RN [7]
RP INTERACTION WITH RAC3.
RX PubMed=9852280; DOI=10.3892/ijmm.1.4.665;
RA Haataja L., Groffen J., Heisterkamp N.;
RT "Identification of a novel Rac3-interacting protein C1D.";
RL Int. J. Mol. Med. 1:665-670(1998).
RN [8]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=10362552; DOI=10.1242/jcs.112.13.2223;
RA Rothbarth K., Spiess E., Juodka B., Yavuzer U., Nehls P., Stammer H.,
RA Werner D.;
RT "Induction of apoptosis by overexpression of the DNA-binding and DNA-PK-
RT activating protein C1D.";
RL J. Cell Sci. 112:2223-2232(1999).
RN [9]
RP FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH TSNAX.
RX PubMed=11801738; DOI=10.1242/jcs.115.1.207;
RA Erdemir T., Bilican B., Oncel D., Goding C.R., Yavuzer U.;
RT "DNA damage-dependent interaction of the nuclear matrix protein C1D with
RT Translin-associated factor X (TRAX).";
RL J. Cell Sci. 115:207-216(2002).
RN [10]
RP FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH EXOSC10.
RX PubMed=17412707; DOI=10.1093/nar/gkm082;
RA Schilders G., van Dijk E., Pruijn G.J.M.;
RT "C1D and hMtr4p associate with the human exosome subunit PM/Scl-100 and are
RT involved in pre-rRNA processing.";
RL Nucleic Acids Res. 35:2564-2572(2007).
RN [11]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-119, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25772364; DOI=10.1016/j.celrep.2015.02.033;
RA Hendriks I.A., Treffers L.W., Verlaan-de Vries M., Olsen J.V.,
RA Vertegaal A.C.;
RT "SUMO-2 orchestrates chromatin modifiers in response to DNA damage.";
RL Cell Rep. 10:1778-1791(2015).
RN [12]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-119; LYS-126 AND LYS-132, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=28112733; DOI=10.1038/nsmb.3366;
RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
RA Nielsen M.L.;
RT "Site-specific mapping of the human SUMO proteome reveals co-modification
RT with phosphorylation.";
RL Nat. Struct. Mol. Biol. 24:325-336(2017).
CC -!- FUNCTION: Plays a role in the recruitment of the RNA exosome complex to
CC pre-rRNA to mediate the 3'-5' end processing of the 5.8S rRNA; this
CC function may include MPHOSPH6. Can activate PRKDC not only in the
CC presence of linear DNA but also in the presence of supercoiled DNA. Can
CC induce apoptosis in a p53/TP53 dependent manner. May regulate the
CC TRAX/TSN complex formation. Potentiates transcriptional repression by
CC NR1D1 and THRB (By similarity). {ECO:0000250,
CC ECO:0000269|PubMed:10362552, ECO:0000269|PubMed:11801738,
CC ECO:0000269|PubMed:17412707, ECO:0000269|PubMed:9679063}.
CC -!- SUBUNIT: Monomer and homodimer. Interacts with NR1D1, THRA, THRB, NCOR1
CC and NCOR2 (By similarity). Interacts with EXOSC10; the interaction
CC probably mediates the association with the nuclear form of the RNA
CC exosome. The homodimeric form interacts with TSNAX following gamma-
CC radiation. Interacts with RAC3. {ECO:0000250,
CC ECO:0000269|PubMed:11801738, ECO:0000269|PubMed:17412707,
CC ECO:0000269|PubMed:9469821, ECO:0000269|PubMed:9679063,
CC ECO:0000269|PubMed:9852280}.
CC -!- INTERACTION:
CC Q13901; P55212: CASP6; NbExp=3; IntAct=EBI-3844053, EBI-718729;
CC Q13901; Q01780: EXOSC10; NbExp=5; IntAct=EBI-3844053, EBI-358236;
CC Q13901; O15499: GSC2; NbExp=3; IntAct=EBI-3844053, EBI-19954058;
CC Q13901; O00291: HIP1; NbExp=3; IntAct=EBI-3844053, EBI-473886;
CC Q13901; P42858: HTT; NbExp=6; IntAct=EBI-3844053, EBI-466029;
CC Q13901; Q5VWK5: IL23R; NbExp=3; IntAct=EBI-3844053, EBI-10248005;
CC Q13901; P13473-2: LAMP2; NbExp=3; IntAct=EBI-3844053, EBI-21591415;
CC Q13901; P62826: RAN; NbExp=3; IntAct=EBI-3844053, EBI-286642;
CC Q13901; Q9Y371: SH3GLB1; NbExp=6; IntAct=EBI-3844053, EBI-2623095;
CC Q13901; P51687: SUOX; NbExp=3; IntAct=EBI-3844053, EBI-3921347;
CC Q13901; O76024: WFS1; NbExp=3; IntAct=EBI-3844053, EBI-720609;
CC Q13901; Q8N5A5-2: ZGPAT; NbExp=3; IntAct=EBI-3844053, EBI-10183064;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11801738}. Cytoplasm
CC {ECO:0000269|PubMed:11801738}. Nucleus, nucleolus
CC {ECO:0000269|PubMed:17412707}. Note=EXOSC10 is required for nucleolar
CC localization (PubMed:17412707). Colocalizes with TSNAX in the nucleus
CC (PubMed:11801738). {ECO:0000269|PubMed:11801738,
CC ECO:0000269|PubMed:17412707}.
CC -!- TISSUE SPECIFICITY: Ubiquitous. Expressed at very high levels in the
CC hippocampus, medulla oblongata, mammary gland, thyroid and salivary
CC gland. Expressed at high levels in the fetal; lung, liver and kidney.
CC Expressed at low levels in skeletal muscle, appendix, heart, lung and
CC colon. {ECO:0000269|PubMed:10362552}.
CC -!- INDUCTION: By gamma-radiation. {ECO:0000269|PubMed:9679063}.
CC -!- PTM: Phosphorylated by PRKDC. {ECO:0000269|PubMed:9679063}.
CC -!- SIMILARITY: Belongs to the C1D family. {ECO:0000305}.
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DR EMBL; X95592; CAA64845.1; -; mRNA.
DR EMBL; AK290451; BAF83140.1; -; mRNA.
DR EMBL; AC079112; AAX88887.1; -; Genomic_DNA.
DR EMBL; CH471053; EAW99884.1; -; Genomic_DNA.
DR EMBL; CH471053; EAW99885.1; -; Genomic_DNA.
DR EMBL; BC005235; AAH05235.1; -; mRNA.
DR EMBL; BC009584; AAH09584.1; -; mRNA.
DR EMBL; BC009589; AAH09589.1; -; mRNA.
DR EMBL; BC016284; AAH16284.1; -; mRNA.
DR CCDS; CCDS1883.1; -.
DR RefSeq; NP_001177192.1; NM_001190263.1.
DR RefSeq; NP_001177194.1; NM_001190265.1.
DR RefSeq; NP_006324.1; NM_006333.3.
DR RefSeq; NP_775269.1; NM_173177.2.
DR AlphaFoldDB; Q13901; -.
DR SMR; Q13901; -.
DR BioGRID; 115705; 53.
DR CORUM; Q13901; -.
DR IntAct; Q13901; 37.
DR MINT; Q13901; -.
DR STRING; 9606.ENSP00000348107; -.
DR iPTMnet; Q13901; -.
DR PhosphoSitePlus; Q13901; -.
DR BioMuta; C1D; -.
DR DMDM; 74754472; -.
DR EPD; Q13901; -.
DR jPOST; Q13901; -.
DR MassIVE; Q13901; -.
DR MaxQB; Q13901; -.
DR PaxDb; Q13901; -.
DR PeptideAtlas; Q13901; -.
DR PRIDE; Q13901; -.
DR ProteomicsDB; 59719; -.
DR TopDownProteomics; Q13901; -.
DR Antibodypedia; 30893; 299 antibodies from 33 providers.
DR DNASU; 10438; -.
DR Ensembl; ENST00000355848.7; ENSP00000348107.3; ENSG00000197223.12.
DR Ensembl; ENST00000409302.1; ENSP00000386779.1; ENSG00000197223.12.
DR Ensembl; ENST00000410067.8; ENSP00000386468.3; ENSG00000197223.12.
DR GeneID; 10438; -.
DR KEGG; hsa:10438; -.
DR MANE-Select; ENST00000410067.8; ENSP00000386468.3; NM_173177.3; NP_775269.1.
DR UCSC; uc002seb.4; human.
DR CTD; 10438; -.
DR DisGeNET; 10438; -.
DR GeneCards; C1D; -.
DR HGNC; HGNC:29911; C1D.
DR HPA; ENSG00000197223; Low tissue specificity.
DR MIM; 606997; gene.
DR neXtProt; NX_Q13901; -.
DR OpenTargets; ENSG00000197223; -.
DR PharmGKB; PA164717007; -.
DR VEuPathDB; HostDB:ENSG00000197223; -.
DR eggNOG; KOG4835; Eukaryota.
DR GeneTree; ENSGT00390000015405; -.
DR HOGENOM; CLU_064339_4_1_1; -.
DR InParanoid; Q13901; -.
DR OMA; KLMSMPR; -.
DR OrthoDB; 1436833at2759; -.
DR PhylomeDB; Q13901; -.
DR TreeFam; TF314651; -.
DR PathwayCommons; Q13901; -.
DR Reactome; R-HSA-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR SignaLink; Q13901; -.
DR SIGNOR; Q13901; -.
DR BioGRID-ORCS; 10438; 255 hits in 1047 CRISPR screens.
DR ChiTaRS; C1D; human.
DR GeneWiki; C1D; -.
DR GenomeRNAi; 10438; -.
DR Pharos; Q13901; Tbio.
DR PRO; PR:Q13901; -.
DR Proteomes; UP000005640; Chromosome 2.
DR RNAct; Q13901; protein.
DR Bgee; ENSG00000197223; Expressed in islet of Langerhans and 97 other tissues.
DR ExpressionAtlas; Q13901; baseline and differential.
DR Genevisible; Q13901; HS.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0000178; C:exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); TAS:UniProtKB.
DR GO; GO:0005730; C:nucleolus; IDA:HPA.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR GO; GO:0005634; C:nucleus; TAS:ProtInc.
DR GO; GO:0017053; C:transcription repressor complex; IEA:Ensembl.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0016922; F:nuclear receptor binding; IEA:Ensembl.
DR GO; GO:0003723; F:RNA binding; IDA:UniProtKB.
DR GO; GO:0003714; F:transcription corepressor activity; IEA:Ensembl.
DR GO; GO:0006915; P:apoptotic process; IEA:UniProtKB-KW.
DR GO; GO:0000460; P:maturation of 5.8S rRNA; IMP:UniProtKB.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR InterPro; IPR011082; Exosome-assoc_fac/DNA_repair.
DR InterPro; IPR007146; Sas10/Utp3/C1D.
DR PANTHER; PTHR15341; PTHR15341; 1.
DR Pfam; PF04000; Sas10_Utp3; 1.
PE 1: Evidence at protein level;
KW Apoptosis; Cytoplasm; DNA-binding; Isopeptide bond; Nucleus;
KW Phosphoprotein; Reference proteome; Repressor; RNA-binding;
KW rRNA processing; Transcription; Transcription regulation; Ubl conjugation.
FT CHAIN 1..141
FT /note="Nuclear nucleic acid-binding protein C1D"
FT /id="PRO_0000316300"
FT REGION 1..100
FT /note="Required for transcriptional repression"
FT /evidence="ECO:0000250"
FT REGION 50..100
FT /note="Interaction with NR1D1"
FT /evidence="ECO:0000250"
FT REGION 100..141
FT /note="Interaction with NCOR1 and NCOR2"
FT /evidence="ECO:0000250"
FT CROSSLNK 119
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:25772364,
FT ECO:0007744|PubMed:28112733"
FT CROSSLNK 126
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 132
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT VARIANT 127
FT /note="S -> P (in dbSNP:rs10444)"
FT /id="VAR_053990"
FT CONFLICT 76
FT /note="V -> I (in Ref. 2; BAF83140)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 141 AA; 16019 MW; 9976A3BBD5620D63 CRC64;
MAGEEINEDY PVEIHEYLSA FENSIGAVDE MLKTMMSVSR NELLQKLDPL EQAKVDLVSA
YTLNSMFWVY LATQGVNPKE HPVKQELERI RVYMNRVKEI TDKKKAGKLD RGAASRFVKN
ALWEPKSKNA SKVANKGKSK S
