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5vyc

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{{Large structure}}
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==Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1.==
==Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1.==
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<StructureSection load='5vyc' size='340' side='right' caption='[[5vyc]], [[Resolution|resolution]] 6.00&Aring;' scene=''>
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<StructureSection load='5vyc' size='340' side='right'caption='[[5vyc]], [[Resolution|resolution]] 6.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5vyc]] is a 222 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VYC FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5vyc]] is a 60 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VYC FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 6&#8491;</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5vyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyc OCA], [http://pdbe.org/5vyc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vyc RCSB], [http://www.ebi.ac.uk/pdbsum/5vyc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyc ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5vyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyc OCA], [https://pdbe.org/5vyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vyc RCSB], [https://www.ebi.ac.uk/pdbsum/5vyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyc ProSAT]</span></td></tr>
</table>
</table>
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{{Large structure}}
 
== Disease ==
== Disease ==
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[[http://www.uniprot.org/uniprot/RS17_HUMAN RS17_HUMAN]] Blackfan-Diamond disease. Diamond-Blackfan anemia 4 (DBA4) [MIM:[http://omim.org/entry/612527 612527]]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of developing leukemia. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:17647292</ref> <ref>PMID:19061985</ref> [[http://www.uniprot.org/uniprot/RS24_HUMAN RS24_HUMAN]] Blackfan-Diamond disease. Diamond-Blackfan anemia 3 (DBA3) [MIM:[http://omim.org/entry/610629 610629]]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of developing leukemia. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:17186470</ref> [[http://www.uniprot.org/uniprot/RS19_HUMAN RS19_HUMAN]] Blackfan-Diamond disease. Diamond-Blackfan anemia 1 (DBA1) [MIM:[http://omim.org/entry/105650 105650]]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of developing leukemia. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:17517689</ref> <ref>PMID:12586610</ref> <ref>PMID:9988267</ref> <ref>PMID:10590074</ref> <ref>PMID:11112378</ref> <ref>PMID:12750732</ref> <ref>PMID:15384984</ref> [REFERENCE:18] [[http://www.uniprot.org/uniprot/RS7_HUMAN RS7_HUMAN]] Blackfan-Diamond disease. Diamond-Blackfan anemia 8 (DBA8) [MIM:[http://omim.org/entry/612563 612563]]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:19061985</ref> [[http://www.uniprot.org/uniprot/RS10_HUMAN RS10_HUMAN]] Blackfan-Diamond disease. Diamond-Blackfan anemia 9 (DBA9) [MIM:[http://omim.org/entry/613308 613308]]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:20116044</ref> [[http://www.uniprot.org/uniprot/RS14_HUMAN RS14_HUMAN]] Myelodysplastic syndrome associated with isolated del(5q) chromosome abnormality. [[http://www.uniprot.org/uniprot/RS26_HUMAN RS26_HUMAN]] Blackfan-Diamond disease. Diamond-Blackfan anemia 10 (DBA10) [MIM:[http://omim.org/entry/613309 613309]]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:20116044</ref>
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[https://www.uniprot.org/uniprot/RS19_HUMAN RS19_HUMAN] Blackfan-Diamond disease. Diamond-Blackfan anemia 1 (DBA1) [MIM:[https://omim.org/entry/105650 105650]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of developing leukemia. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:17517689</ref> <ref>PMID:12586610</ref> <ref>PMID:9988267</ref> <ref>PMID:10590074</ref> <ref>PMID:11112378</ref> <ref>PMID:12750732</ref> <ref>PMID:15384984</ref> [REFERENCE:18]
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/RS24_HUMAN RS24_HUMAN]] Required for processing of pre-rRNA and maturation of 40S ribosomal subunits.<ref>PMID:18230666</ref> [[http://www.uniprot.org/uniprot/RS19_HUMAN RS19_HUMAN]] Required for pre-rRNA processing and maturation of 40S ribosomal subunits.<ref>PMID:16990592</ref> [[http://www.uniprot.org/uniprot/RS7_HUMAN RS7_HUMAN]] Required for rRNA maturation.<ref>PMID:19061985</ref> [[http://www.uniprot.org/uniprot/RL41_HUMAN RL41_HUMAN]] Interacts with the beta subunit of protein kinase CKII and stimulates phosphorylation of DNA topoisomerase II alpha by CKII. [[http://www.uniprot.org/uniprot/RS6_HUMAN RS6_HUMAN]] May play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA. [[http://www.uniprot.org/uniprot/RSSA_HUMAN RSSA_HUMAN]] Required for the assembly and/or stability of the 40S ribosomal subunit. Required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits. Also functions as a cell surface receptor for laminin. Plays a role in cell adhesion to the basement membrane and in the consequent activation of signaling transduction pathways. May play a role in cell fate determination and tissue morphogenesis. Acts as a PPP1R16B-dependent substrate of PPP1CA. Also acts as a receptor for several other ligands, including the pathogenic prion protein, viruses, and bacteria.<ref>PMID:6300843</ref> <ref>PMID:16263087</ref> <ref>PMID:15516338</ref> [[http://www.uniprot.org/uniprot/RS3A_HUMAN RS3A_HUMAN]] May play a role during erythropoiesis through regulation of transcription factor DDIT3 (By similarity).[HAMAP-Rule:MF_03122] [[http://www.uniprot.org/uniprot/RS10_HUMAN RS10_HUMAN]] Component of the 40S ribosomal subunit. [[http://www.uniprot.org/uniprot/MCTS1_HUMAN MCTS1_HUMAN]] Anti-oncogene that play a role in cell cycle regulation; decreases cell doubling time and anchorage-dependent growth; shortens the duration of G1 transit time and G1/S transition. When constituvely expressed, increases CDK4 and CDK6 kinases activity and CCND1/cyclin D1 protein level, as well as G1 cyclin/CDK complex formation. Plays a role as translation enhancer; Recruits the density-regulated protein/DENR and binds to the cap complex of the 5'-terminus of mRNAs, subsequently altering the mRNA translation profile; Up-regulates protein levels of BCL2L2, TFDP1, MRE11A, CCND1 and E2F1, while mRNA levels remains constant. Hyperactivates DNA damage signaling pathway; increased gamma-irradiation-induced phosphorylation of histone H2AX, and induces damage foci formation. Increases the overall number of chromosomal abnormalities such as larger chromosomes formation and multiples chromosomal fusions when overexpressed in gamma-irradiated cells. May play a role in promoting lymphoid tumor development: lymphoid cell lines overexpressing MCTS1 exhibit increased growth rates and display increased protection against apoptosis. May contribute to the pathogenesis and progression of breast cancer via promotion of angiogenesis through the decline of inhibitory THBS1/thrombospondin-1, and inhibition of apoptosis. Involved in the process of proteasome degradation to down-regulate Tumor suppressor p53/TP53 in breast cancer cell; Positively regulates phosphorylation of MAPK1 and MAPK3.<ref>PMID:9766643</ref> <ref>PMID:10440924</ref> <ref>PMID:11709712</ref> <ref>PMID:12637315</ref> <ref>PMID:16322206</ref> <ref>PMID:15897892</ref> <ref>PMID:16982740</ref> <ref>PMID:17416211</ref> <ref>PMID:17016429</ref> [[http://www.uniprot.org/uniprot/RACK1_HUMAN RACK1_HUMAN]] Involved in the recruitment, assembly and/or regulation of a variety of signaling molecules. Interacts with a wide variety of proteins and plays a role in many cellular processes. Component of the 40S ribosomal subunit involved in translational repression. Binds to and stabilizes activated protein kinase C (PKC), increasing PKC-mediated phosphorylation. May recruit activated PKC to the ribosome, leading to phosphorylation of EIF6. Inhibits the activity of SRC kinases including SRC, LCK and YES1. Inhibits cell growth by prolonging the G0/G1 phase of the cell cycle. Enhances phosphorylation of BMAL1 by PRKCA and inhibits transcriptional activity of the BMAL1-CLOCK heterodimer. Facilitates ligand-independent nuclear translocation of AR following PKC activation, represses AR transactivation activity and is required for phosphorylation of AR by SRC. Modulates IGF1R-dependent integrin signaling and promotes cell spreading and contact with the extracellular matrix. Involved in PKC-dependent translocation of ADAM12 to the cell membrane. Promotes the ubiquitination and proteasome-mediated degradation of proteins such as CLEC1B and HIF1A. Required for VANGL2 membrane localization, inhibits Wnt signaling, and regulates cellular polarization and oriented cell division during gastrulation. Required for PTK2/FAK1 phosphorylation and dephosphorylation. Regulates internalization of the muscarinic receptor CHRM2. Promotes apoptosis by increasing oligomerization of BAX and disrupting the interaction of BAX with the anti-apoptotic factor BCL2L. Inhibits TRPM6 channel activity. Regulates cell surface expression of some GPCRs such as TBXA2R. Plays a role in regulation of FLT1-mediated cell migration. Involved in the transport of ABCB4 from the Golgi to the apical bile canalicular membrane (PubMed:19674157). Binds to Y.pseudotuberculosis yopK which leads to inhibition of phagocytosis and survival of bacteria following infection of host cells. Enhances phosphorylation of HIV-1 Nef by PKCs. Promotes migration of breast carcinoma cells by binding to and activating RHOA.<ref>PMID:11312657</ref> <ref>PMID:11884618</ref> <ref>PMID:12589061</ref> <ref>PMID:12958311</ref> <ref>PMID:17108144</ref> <ref>PMID:17244529</ref> <ref>PMID:17956333</ref> <ref>PMID:18088317</ref> <ref>PMID:18258429</ref> <ref>PMID:18621736</ref> <ref>PMID:19423701</ref> <ref>PMID:19674157</ref> <ref>PMID:19785988</ref> <ref>PMID:20499158</ref> <ref>PMID:20541605</ref> <ref>PMID:20573744</ref> <ref>PMID:20976005</ref> <ref>PMID:21212275</ref> <ref>PMID:21347310</ref> <ref>PMID:9584165</ref> [[http://www.uniprot.org/uniprot/RS18_HUMAN RS18_HUMAN]] Located at the top of the head of the 40S subunit, it contacts several helices of the 18S rRNA (By similarity).[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/DENR_HUMAN DENR_HUMAN]] May be involved in the translation of target mRNAs by scanning and recognition of the initiation codon. Involved in translation initiation; promotes recruitmnet of aminoacetyled initiator tRNA to P site of 40S ribosomes. Can promote release of deacylated tRNA and mRNA from recycled 40S subunits following ABCE1-mediated dissociation of post-termination ribosomal complexes into subunits. Plays a role in the modulation of the translational profile of a subset of cancer-related mRNAs when recruited to the translational initiation complex by the oncogene MCTS1.<ref>PMID:16982740</ref> <ref>PMID:17878526</ref> <ref>PMID:20713520</ref>
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[https://www.uniprot.org/uniprot/RS19_HUMAN RS19_HUMAN] Required for pre-rRNA processing and maturation of 40S ribosomal subunits.<ref>PMID:16990592</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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</div>
</div>
<div class="pdbe-citations 5vyc" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 5vyc" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Ribosome 3D structures|Ribosome 3D structures]]
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*[[3D sructureseceptor for activated protein kinase C 1|3D sructureseceptor for activated protein kinase C 1]]
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Dmitriev, S E]]
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[[Category: Large Structures]]
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[[Category: Garber, M B]]
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[[Category: Dmitriev SE]]
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[[Category: Lomakin, I B]]
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[[Category: Garber MB]]
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[[Category: Steitz, T A]]
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[[Category: Lomakin IB]]
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[[Category: Stolboushkina, E A]]
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[[Category: Steitz TA]]
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[[Category: Vaidya, A T]]
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[[Category: Stolboushkina EA]]
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[[Category: 40s subunit]]
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[[Category: Vaidya AT]]
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[[Category: Denr-mct-1]]
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[[Category: Pua]]
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[[Category: Ribosome]]
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Current revision

Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1.

PDB ID 5vyc

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