PHF13_HUMAN
ID PHF13_HUMAN Reviewed; 300 AA.
AC Q86YI8; B3KUQ7; Q59FB6; Q5TH65; Q8N551; Q9UJP2;
DT 15-AUG-2003, integrated into UniProtKB/Swiss-Prot.
DT 05-MAY-2009, sequence version 2.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=PHD finger protein 13;
DE AltName: Full=Survival time-associated PHD finger protein in ovarian cancer 1;
DE Short=SPOC1;
GN Name=PHF13;
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 [LARGE SCALE MRNA].
RC TISSUE=Testis;
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 [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain;
RA Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.,
RA Ohara O., Nagase T., Kikuno R.F.;
RT "Homo sapiens protein coding cDNA.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16710414; DOI=10.1038/nature04727;
RA Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A.,
RA Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C.,
RA Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.,
RA Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C.,
RA Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W.,
RA Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J.,
RA Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J.,
RA Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y.,
RA Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J.,
RA Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
RA Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
RA Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
RA Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S.,
RA Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K.,
RA Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R.,
RA Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M.,
RA Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S.,
RA Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J.,
RA Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W.,
RA McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
RA Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
RA Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
RA Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
RA Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S.,
RA Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M.,
RA White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H.,
RA Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E.,
RA Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G.,
RA Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.;
RT "The DNA sequence and biological annotation of human chromosome 1.";
RL Nature 441:315-321(2006).
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 (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT GLU-20.
RC TISSUE=Lung, and Testis;
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 48-300.
RA Rhodes S., Huckle E.;
RL Submitted (OCT-1999) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH GSK3B, PROTEASOMAL
RP DEGRADATION, AND INDUCTION.
RX PubMed=19638409; DOI=10.1242/jcs.047365;
RA Kinkley S., Staege H., Mohrmann G., Rohaly G., Schaub T., Kremmer E.,
RA Winterpacht A., Will H.;
RT "SPOC1: a novel PHD-containing protein modulating chromatin structure and
RT mitotic chromosome condensation.";
RL J. Cell Sci. 122:2946-2956(2009).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.67 ANGSTROMS) OF 250-300 IN COMPLEX WITH
RP TRIMETHYLATED HISTONE H3 AND ZINC IONS, AND X-RAY CRYSTALLOGRAPHY (1.85
RP ANGSTROMS) OF 232-281.
RG Structural genomics consortium (SGC);
RT "Crystal structure of PHF13 in complex with tri-methylated histone H3K4.";
RL Submitted (SEP-2010) to the PDB data bank.
CC -!- FUNCTION: Modulates chromatin structure. Required for normal chromosome
CC condensation during the early stages of mitosis. Required for normal
CC chromosome separation during mitosis. {ECO:0000269|PubMed:19638409}.
CC -!- SUBUNIT: Interacts with histone H3 that is trimethylated at 'Lys-4'
CC (H3K4me3). Interacts with GSK3B. {ECO:0000269|PubMed:19638409,
CC ECO:0000269|Ref.8}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19638409}. Nucleus,
CC nucleoplasm {ECO:0000269|PubMed:19638409}. Note=Predominantly bound to
CC chromatin, but a minor proportion is also detected in the nucleoplasm.
CC -!- INDUCTION: Expression levels are tightly regulated during the cell
CC cycle. Strongly up-regulated during late G2 phase and M phase of the
CC mitotic cell cycle. Down-regulated at the G1-S phase transition of the
CC cell cycle. {ECO:0000269|PubMed:19638409}.
CC -!- PTM: Subject to proteasomal degradation. Stable when bound to
CC chromatin. The soluble form is rapidly degraded.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH32792.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAD92781.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AK315110; BAG37568.1; -; mRNA.
DR EMBL; AK097715; BAG53519.1; -; mRNA.
DR EMBL; AB209544; BAD92781.1; ALT_INIT; mRNA.
DR EMBL; AL031447; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471130; EAW71561.1; -; Genomic_DNA.
DR EMBL; BC032792; AAH32792.2; ALT_INIT; mRNA.
DR EMBL; BC038516; AAH38516.1; -; mRNA.
DR EMBL; AL121733; CAB57324.1; -; mRNA.
DR CCDS; CCDS85.1; -.
DR RefSeq; NP_722519.2; NM_153812.2.
DR PDB; 3O70; X-ray; 1.85 A; A=232-281.
DR PDB; 3O7A; X-ray; 1.67 A; A=229-280.
DR PDBsum; 3O70; -.
DR PDBsum; 3O7A; -.
DR AlphaFoldDB; Q86YI8; -.
DR SMR; Q86YI8; -.
DR BioGRID; 127151; 10.
DR IntAct; Q86YI8; 6.
DR MINT; Q86YI8; -.
DR STRING; 9606.ENSP00000366876; -.
DR BindingDB; Q86YI8; -.
DR ChEMBL; CHEMBL1764945; -.
DR iPTMnet; Q86YI8; -.
DR PhosphoSitePlus; Q86YI8; -.
DR BioMuta; PHF13; -.
DR DMDM; 229462750; -.
DR EPD; Q86YI8; -.
DR MassIVE; Q86YI8; -.
DR PaxDb; Q86YI8; -.
DR PeptideAtlas; Q86YI8; -.
DR PRIDE; Q86YI8; -.
DR ProteomicsDB; 70418; -.
DR Antibodypedia; 13124; 142 antibodies from 20 providers.
DR DNASU; 148479; -.
DR Ensembl; ENST00000377648.5; ENSP00000366876.4; ENSG00000116273.6.
DR GeneID; 148479; -.
DR KEGG; hsa:148479; -.
DR MANE-Select; ENST00000377648.5; ENSP00000366876.4; NM_153812.3; NP_722519.2.
DR UCSC; uc001aob.5; human.
DR CTD; 148479; -.
DR DisGeNET; 148479; -.
DR GeneCards; PHF13; -.
DR HGNC; HGNC:22983; PHF13.
DR HPA; ENSG00000116273; Low tissue specificity.
DR neXtProt; NX_Q86YI8; -.
DR OpenTargets; ENSG00000116273; -.
DR PharmGKB; PA134901883; -.
DR VEuPathDB; HostDB:ENSG00000116273; -.
DR eggNOG; KOG1844; Eukaryota.
DR GeneTree; ENSGT00530000063882; -.
DR HOGENOM; CLU_047981_0_0_1; -.
DR InParanoid; Q86YI8; -.
DR OMA; HAFQSEG; -.
DR OrthoDB; 982722at2759; -.
DR PhylomeDB; Q86YI8; -.
DR TreeFam; TF331373; -.
DR PathwayCommons; Q86YI8; -.
DR SignaLink; Q86YI8; -.
DR BioGRID-ORCS; 148479; 24 hits in 1082 CRISPR screens.
DR ChiTaRS; PHF13; human.
DR EvolutionaryTrace; Q86YI8; -.
DR GenomeRNAi; 148479; -.
DR Pharos; Q86YI8; Tbio.
DR PRO; PR:Q86YI8; -.
DR Proteomes; UP000005640; Chromosome 1.
DR RNAct; Q86YI8; protein.
DR Bgee; ENSG00000116273; Expressed in secondary oocyte and 190 other tissues.
DR ExpressionAtlas; Q86YI8; baseline and differential.
DR Genevisible; Q86YI8; HS.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035064; F:methylated histone binding; NAS:UniProtKB.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0007059; P:chromosome segregation; IMP:UniProtKB.
DR GO; GO:0000278; P:mitotic cell cycle; IMP:UniProtKB.
DR GO; GO:0007076; P:mitotic chromosome condensation; IMP:UniProtKB.
DR CDD; cd15632; PHD_PHF13; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR041947; PHD_PHF13.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF00628; PHD; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell cycle; Cell division; Chromatin regulator;
KW DNA condensation; Metal-binding; Mitosis; Nucleus; Reference proteome;
KW Zinc; Zinc-finger.
FT CHAIN 1..300
FT /note="PHD finger protein 13"
FT /id="PRO_0000059304"
FT ZN_FING 232..280
FT /note="PHD-type"
FT REGION 109..185
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 241..248
FT /note="Interaction with trimethylated histone H3 (H3K4)"
FT MOTIF 110..127
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000305"
FT COMPBIAS 151..185
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VARIANT 20
FT /note="K -> E (in dbSNP:rs17853850)"
FT /evidence="ECO:0000269|PubMed:15489334"
FT /id="VAR_055285"
FT CONFLICT 111
FT /note="K -> R (in Ref. 1; BAG53519)"
FT /evidence="ECO:0000305"
FT STRAND 246..248
FT /evidence="ECO:0007829|PDB:3O7A"
FT TURN 250..252
FT /evidence="ECO:0007829|PDB:3O7A"
FT STRAND 255..257
FT /evidence="ECO:0007829|PDB:3O7A"
FT TURN 258..262
FT /evidence="ECO:0007829|PDB:3O7A"
FT HELIX 265..267
FT /evidence="ECO:0007829|PDB:3O7A"
FT HELIX 275..278
FT /evidence="ECO:0007829|PDB:3O7A"
SQ SEQUENCE 300 AA; 33582 MW; 197663A113B995F2 CRC64;
MDSDSCAAAF HPEEYSPSCK RRRTVEDFNK FCTFVLAYAG YIPYPKEELP LRSSPSPANS
TAGTIDSDGW DAGFSDIASS VPLPVSDRCF SHLQPTLLQR AKPSNFLLDR KKTDKLKKKK
KRKRRDSDAP GKEGYRGGLL KLEAADPYVE TPTSPTLQDI PQAPSDPCSG WDSDTPSSGS
CATVSPDQVK EIKTEGKRTI VRQGKQVVFR DEDSTGNDED IMVDSDDDSW DLVTCFCMKP
FAGRPMIECN ECHTWIHLSC AKIRKSNVPE VFVCQKCRDS KFDIRRSNRS RTGSRKLFLD
