NIP7_HUMAN
ID NIP7_HUMAN Reviewed; 180 AA.
AC Q9Y221; B2RD04; Q9NZZ0;
DT 07-DEC-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 178.
DE RecName: Full=60S ribosome subunit biogenesis protein NIP7 homolog;
DE AltName: Full=KD93;
DE AltName: Full=Nucleolar pre-rRNA processing protein NIP7;
GN Name=NIP7; ORFNames=CGI-37, HSPC031, HSPC180, OK/SW-cl.76, OK/SW-cl.78;
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] (ISOFORM 1).
RX PubMed=10810093; DOI=10.1101/gr.10.5.703;
RA Lai C.-H., Chou C.-Y., Ch'ang L.-Y., Liu C.-S., Lin W.-C.;
RT "Identification of novel human genes evolutionarily conserved in
RT Caenorhabditis elegans by comparative proteomics.";
RL Genome Res. 10:703-713(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Umbilical cord blood;
RX PubMed=11042152; DOI=10.1101/gr.140200;
RA Zhang Q.-H., Ye M., Wu X.-Y., Ren S.-X., Zhao M., Zhao C.-J., Fu G.,
RA Shen Y., Fan H.-Y., Lu G., Zhong M., Xu X.-R., Han Z.-G., Zhang J.-W.,
RA Tao J., Huang Q.-H., Zhou J., Hu G.-X., Gu J., Chen S.-J., Chen Z.;
RT "Cloning and functional analysis of cDNAs with open reading frames for 300
RT previously undefined genes expressed in CD34+ hematopoietic stem/progenitor
RT cells.";
RL Genome Res. 10:1546-1560(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Colon adenocarcinoma;
RA Shichijo S., Itoh K.;
RT "Identification of immuno-peptidmics that are recognized by tumor-reactive
RT CTL generated from TIL of colon cancer patients.";
RL Submitted (MAY-2001) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RC TISSUE=Periodontal ligament;
RA Myokai F.;
RT "Mechanical stress-induced gene 26-1, 26-2.";
RL Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [6]
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 [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Skin;
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 [8]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=12429849; DOI=10.1091/mbc.e02-05-0271;
RA Scherl A., Coute Y., Deon C., Calle A., Kindbeiter K., Sanchez J.-C.,
RA Greco A., Hochstrasser D.F., Diaz J.-J.;
RT "Functional proteomic analysis of human nucleolus.";
RL Mol. Biol. Cell 13:4100-4109(2002).
RN [9]
RP INTERACTION WITH NOL8.
RX PubMed=14660641; DOI=10.1074/jbc.m305935200;
RA Sekiguchi T., Todaka Y., Wang Y., Hirose E., Nakashima N., Nishimoto T.;
RT "A novel human nucleolar protein, Nop132, binds to the G proteins, RRAG
RT A/C/D.";
RL J. Biol. Chem. 279:8343-8350(2004).
RN [10]
RP INTERACTION WITH SBDS.
RX PubMed=17643419; DOI=10.1016/j.yexcr.2007.06.024;
RA Hesling C., Oliveira C.C., Castilho B.A., Zanchin N.I.;
RT "The Shwachman-Bodian-Diamond syndrome associated protein interacts with
RT HsNip7 and its down-regulation affects gene expression at the
RT transcriptional and translational levels.";
RL Exp. Cell Res. 313:4180-4195(2007).
RN [11]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [12]
RP FUNCTION, INTERACTION WITH FTSJ3, AND SUBCELLULAR LOCATION.
RX PubMed=22195017; DOI=10.1371/journal.pone.0029174;
RA Morello L.G., Coltri P.P., Quaresma A.J., Simabuco F.M., Silva T.C.,
RA Singh G., Nickerson J.A., Oliveira C.C., Moore M.J., Zanchin N.I.;
RT "The human nucleolar protein FTSJ3 associates with NIP7 and functions in
RT pre-rRNA processing.";
RL PLoS ONE 6:E29174-E29174(2011).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), DOMAINS, SUBUNIT STRUCTURE, AND
RP TISSUE SPECIFICITY.
RX PubMed=15522784; DOI=10.1016/j.jsb.2004.06.010;
RA Liu J.-F., Wang X.-Q., Wang Z.-X., Chen J.-R., Jiang T., An X.-M.,
RA Chang W.-R., Liang D.-C.;
RT "Crystal structure of KD93, a novel protein expressed in human
RT hematopoietic stem/progenitor cells.";
RL J. Struct. Biol. 148:370-374(2004).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
RA Kuzin A.P., Chen Y., Forouhar F., Acton T.B., Shastry R., Ma L.-C.,
RA Cooper B., Xiao R., Montelione G., Tong L., Hunt J.F.;
RT "Crystal structure of Northeast structural genomics consortium target
RT HR2118: a human homolog of Saccharomyces cerevisiae NIP7p.";
RL Submitted (JUN-2004) to the PDB data bank.
RN [15]
RP VARIANT [LARGE SCALE ANALYSIS] GLN-171.
RX PubMed=16959974; DOI=10.1126/science.1133427;
RA Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D.,
RA Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P.,
RA Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V.,
RA Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H.,
RA Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W.,
RA Velculescu V.E.;
RT "The consensus coding sequences of human breast and colorectal cancers.";
RL Science 314:268-274(2006).
CC -!- FUNCTION: Required for proper 34S pre-rRNA processing and 60S ribosome
CC subunit assembly. {ECO:0000269|PubMed:22195017}.
CC -!- SUBUNIT: Monomer. Interacts with pre-ribosome complex. May bind to RNA
CC (By similarity). Interacts with NOL8. May interact with SBDS. Interacts
CC with FTSJ3. {ECO:0000250, ECO:0000269|PubMed:14660641,
CC ECO:0000269|PubMed:15522784, ECO:0000269|PubMed:17643419,
CC ECO:0000269|PubMed:22195017}.
CC -!- INTERACTION:
CC Q9Y221; O43186: CRX; NbExp=3; IntAct=EBI-749003, EBI-748171;
CC Q9Y221; Q9BRK4: LZTS2; NbExp=3; IntAct=EBI-749003, EBI-741037;
CC Q9Y221; Q7Z6G3-2: NECAB2; NbExp=3; IntAct=EBI-749003, EBI-10172876;
CC Q9Y221; Q96CV9: OPTN; NbExp=3; IntAct=EBI-749003, EBI-748974;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:12429849,
CC ECO:0000269|PubMed:22195017}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9Y221-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9Y221-2; Sequence=VSP_012094;
CC -!- TISSUE SPECIFICITY: Expressed in hematopoietic stem/progenitor cells.
CC {ECO:0000269|PubMed:15522784}.
CC -!- SIMILARITY: Belongs to the NIP7 family. {ECO:0000305}.
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DR EMBL; AF132971; AAD27746.1; -; mRNA.
DR EMBL; AF085360; AAD40195.1; -; mRNA.
DR EMBL; AF161528; AAF29143.1; -; mRNA.
DR EMBL; AB062398; BAB93485.1; -; mRNA.
DR EMBL; AB062479; BAB93504.1; -; mRNA.
DR EMBL; AB112439; BAD05056.1; -; mRNA.
DR EMBL; AK315355; BAG37751.1; -; mRNA.
DR EMBL; CH471092; EAW83271.1; -; Genomic_DNA.
DR EMBL; BC015941; AAH15941.1; -; mRNA.
DR CCDS; CCDS10877.1; -. [Q9Y221-1]
DR CCDS; CCDS56003.1; -. [Q9Y221-2]
DR RefSeq; NP_001186363.1; NM_001199434.1. [Q9Y221-2]
DR RefSeq; NP_057185.1; NM_016101.4. [Q9Y221-1]
DR PDB; 1SQW; X-ray; 1.90 A; A=1-180.
DR PDB; 1T5Y; X-ray; 2.50 A; A=1-180.
DR PDBsum; 1SQW; -.
DR PDBsum; 1T5Y; -.
DR AlphaFoldDB; Q9Y221; -.
DR SMR; Q9Y221; -.
DR BioGRID; 119517; 175.
DR IntAct; Q9Y221; 34.
DR MINT; Q9Y221; -.
DR STRING; 9606.ENSP00000254940; -.
DR DrugBank; DB12339; Radezolid.
DR iPTMnet; Q9Y221; -.
DR MetOSite; Q9Y221; -.
DR PhosphoSitePlus; Q9Y221; -.
DR SwissPalm; Q9Y221; -.
DR BioMuta; NIP7; -.
DR DMDM; 56404676; -.
DR SWISS-2DPAGE; Q9Y221; -.
DR EPD; Q9Y221; -.
DR jPOST; Q9Y221; -.
DR MassIVE; Q9Y221; -.
DR MaxQB; Q9Y221; -.
DR PaxDb; Q9Y221; -.
DR PeptideAtlas; Q9Y221; -.
DR PRIDE; Q9Y221; -.
DR ProteomicsDB; 85597; -. [Q9Y221-1]
DR ProteomicsDB; 85598; -. [Q9Y221-2]
DR TopDownProteomics; Q9Y221-1; -. [Q9Y221-1]
DR Antibodypedia; 16183; 235 antibodies from 31 providers.
DR DNASU; 51388; -.
DR Ensembl; ENST00000254940.10; ENSP00000254940.5; ENSG00000132603.15. [Q9Y221-1]
DR Ensembl; ENST00000254941.6; ENSP00000254941.6; ENSG00000132603.15. [Q9Y221-2]
DR GeneID; 51388; -.
DR KEGG; hsa:51388; -.
DR MANE-Select; ENST00000254940.10; ENSP00000254940.5; NM_016101.5; NP_057185.1.
DR UCSC; uc002exa.4; human. [Q9Y221-1]
DR CTD; 51388; -.
DR DisGeNET; 51388; -.
DR GeneCards; NIP7; -.
DR HGNC; HGNC:24328; NIP7.
DR HPA; ENSG00000132603; Low tissue specificity.
DR MIM; 619204; gene.
DR neXtProt; NX_Q9Y221; -.
DR OpenTargets; ENSG00000132603; -.
DR PharmGKB; PA142671264; -.
DR VEuPathDB; HostDB:ENSG00000132603; -.
DR eggNOG; KOG3492; Eukaryota.
DR GeneTree; ENSGT00950000182971; -.
DR HOGENOM; CLU_097217_0_0_1; -.
DR InParanoid; Q9Y221; -.
DR OMA; YKIWVKP; -.
DR OrthoDB; 1405073at2759; -.
DR PhylomeDB; Q9Y221; -.
DR TreeFam; TF300081; -.
DR PathwayCommons; Q9Y221; -.
DR Reactome; R-HSA-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR SignaLink; Q9Y221; -.
DR BioGRID-ORCS; 51388; 810 hits in 1083 CRISPR screens.
DR ChiTaRS; NIP7; human.
DR EvolutionaryTrace; Q9Y221; -.
DR GeneWiki; NIP7; -.
DR GenomeRNAi; 51388; -.
DR Pharos; Q9Y221; Tbio.
DR PRO; PR:Q9Y221; -.
DR Proteomes; UP000005640; Chromosome 16.
DR RNAct; Q9Y221; protein.
DR Bgee; ENSG00000132603; Expressed in secondary oocyte and 180 other tissues.
DR ExpressionAtlas; Q9Y221; baseline and differential.
DR Genevisible; Q9Y221; HS.
DR GO; GO:0005829; C:cytosol; IDA:HPA.
DR GO; GO:0005730; C:nucleolus; IDA:HPA.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR GO; GO:0030687; C:preribosome, large subunit precursor; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; HDA:UniProtKB.
DR GO; GO:0042273; P:ribosomal large subunit biogenesis; IBA:GO_Central.
DR GO; GO:0042255; P:ribosome assembly; IEA:InterPro.
DR Gene3D; 2.30.130.10; -; 1.
DR InterPro; IPR002478; PUA.
DR InterPro; IPR015947; PUA-like_sf.
DR InterPro; IPR036974; PUA_sf.
DR InterPro; IPR016686; Ribosomal_synth_fac_NIP7.
DR InterPro; IPR040598; UPF0113_N.
DR InterPro; IPR005155; UPF0113_PUA.
DR Pfam; PF03657; UPF0113; 1.
DR Pfam; PF17833; UPF0113_N; 1.
DR PIRSF; PIRSF017190; Rbsml_synth_fac_NIP7; 1.
DR SMART; SM00359; PUA; 1.
DR SUPFAM; SSF88697; SSF88697; 1.
DR PROSITE; PS50890; PUA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Nucleus; Reference proteome;
KW Ribosome biogenesis; RNA-binding.
FT CHAIN 1..180
FT /note="60S ribosome subunit biogenesis protein NIP7
FT homolog"
FT /id="PRO_0000218773"
FT DOMAIN 94..170
FT /note="PUA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00161"
FT REGION 1..92
FT /note="N-terminal domain"
FT REGION 93..180
FT /note="C-terminal domain"
FT VAR_SEQ 95..141
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:11042152"
FT /id="VSP_012094"
FT VARIANT 171
FT /note="E -> Q (in a breast cancer sample; somatic
FT mutation)"
FT /evidence="ECO:0000269|PubMed:16959974"
FT /id="VAR_036488"
FT HELIX 6..20
FT /evidence="ECO:0007829|PDB:1SQW"
FT HELIX 21..24
FT /evidence="ECO:0007829|PDB:1SQW"
FT HELIX 25..28
FT /evidence="ECO:0007829|PDB:1SQW"
FT STRAND 33..40
FT /evidence="ECO:0007829|PDB:1SQW"
FT STRAND 43..48
FT /evidence="ECO:0007829|PDB:1SQW"
FT HELIX 49..53
FT /evidence="ECO:0007829|PDB:1SQW"
FT TURN 54..56
FT /evidence="ECO:0007829|PDB:1SQW"
FT HELIX 60..66
FT /evidence="ECO:0007829|PDB:1SQW"
FT STRAND 67..73
FT /evidence="ECO:0007829|PDB:1SQW"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:1SQW"
FT HELIX 83..85
FT /evidence="ECO:0007829|PDB:1SQW"
FT HELIX 86..89
FT /evidence="ECO:0007829|PDB:1SQW"
FT HELIX 90..92
FT /evidence="ECO:0007829|PDB:1SQW"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:1SQW"
FT HELIX 101..107
FT /evidence="ECO:0007829|PDB:1SQW"
FT TURN 108..110
FT /evidence="ECO:0007829|PDB:1SQW"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:1SQW"
FT STRAND 118..121
FT /evidence="ECO:0007829|PDB:1SQW"
FT STRAND 130..135
FT /evidence="ECO:0007829|PDB:1SQW"
FT STRAND 140..148
FT /evidence="ECO:0007829|PDB:1SQW"
FT HELIX 150..155
FT /evidence="ECO:0007829|PDB:1SQW"
FT STRAND 160..168
FT /evidence="ECO:0007829|PDB:1SQW"
FT HELIX 169..171
FT /evidence="ECO:0007829|PDB:1SQW"
SQ SEQUENCE 180 AA; 20463 MW; FC6CFB2250AA4FC9 CRC64;
MRPLTEEETR VMFEKIAKYI GENLQLLVDR PDGTYCFRLH NDRVYYVSEK IMKLAANISG
DKLVSLGTCF GKFTKTHKFR LHVTALDYLA PYAKYKVWIK PGAEQSFLYG NHVLKSGLGR
ITENTSQYQG VVVYSMADIP LGFGVAAKST QDCRKVDPMA IVVFHQADIG EYVRHEETLT
