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4ug0

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==STRUCTURE OF THE HUMAN 80S RIBOSOME==
==STRUCTURE OF THE HUMAN 80S RIBOSOME==
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<StructureSection load='4ug0' size='340' side='right' caption='[[4ug0]]' scene=''>
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<SX load='4ug0' size='340' side='right' viewer='molstar' caption='[[4ug0]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4ug0]] is a 81 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UG0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UG0 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4ug0]] is a 10 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=4UG0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UG0 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ug0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ug0 OCA], [https://pdbe.org/4ug0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ug0 RCSB], [https://www.ebi.ac.uk/pdbsum/4ug0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ug0 ProSAT]</span></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=4ug0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ug0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ug0 RCSB], [http://www.ebi.ac.uk/pdbsum/4ug0 PDBsum]</span></td></tr>
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</table>
</table>
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== Disease ==
 
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[[http://www.uniprot.org/uniprot/RL5_HUMAN RL5_HUMAN]] Blackfan-Diamond disease. Diamond-Blackfan anemia 6 (DBA6) [MIM:[http://omim.org/entry/612561 612561]]: 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> <ref>PMID:19191325</ref> [[http://www.uniprot.org/uniprot/RL26_HUMAN RL26_HUMAN]] Diamond-Blackfan anemia 11 (DBA11) [MIM:[http://omim.org/entry/614900 614900]]: 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:22431104</ref> [[http://www.uniprot.org/uniprot/RL7A_HUMAN RL7A_HUMAN]] Note=Chromosomal recombination involving RPL7A activates the receptor kinase domain of the TRK oncogene. [[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/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/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> [[http://www.uniprot.org/uniprot/RS14_HUMAN RS14_HUMAN]] Myelodysplastic syndrome associated with isolated del(5q) chromosome abnormality. [[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/RL21_HUMAN RL21_HUMAN]] Hypotrichosis simplex. Note=Defects in RPL21 are a cause of generalized hypotrichosis simplex (HTS). A rare form of non-syndromic hereditary hypotrichosis without characteristic hair shaft anomalies. Affected individuals typically show normal hair at birth, but hair loss and thinning of the hair shaft start during early childhood and progress with age.<ref>PMID:21412954</ref> [[http://www.uniprot.org/uniprot/RL11_HUMAN RL11_HUMAN]] Blackfan-Diamond disease. Diamond-Blackfan anemia 7 (DBA7) [MIM:[http://omim.org/entry/612562 612562]]: 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> <ref>PMID:19191325</ref> [[http://www.uniprot.org/uniprot/RL35A_HUMAN RL35A_HUMAN]] Blackfan-Diamond disease. Diamond-Blackfan anemia 5 (DBA5) [MIM:[http://omim.org/entry/612528 612528]]: 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:18535205</ref>
 
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/RL5_HUMAN RL5_HUMAN]] Required for rRNA maturation and formation of the 60S ribosomal subunits. This protein binds 5S RNA.<ref>PMID:19061985</ref> [[http://www.uniprot.org/uniprot/RL23A_HUMAN RL23A_HUMAN]] This protein binds to a specific region on the 26S rRNA (By similarity). [[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/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/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/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/RL40_HUMAN RL40_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref> Ribosomal protein L40 is a component of the 60S subunit of the ribosome.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref> [[http://www.uniprot.org/uniprot/RL10L_HUMAN RL10L_HUMAN]] May play a role in compensating for the inactivated X-linked gene during spermatogenesis. [[http://www.uniprot.org/uniprot/RS10_HUMAN RS10_HUMAN]] Component of the 40S ribosomal subunit. [[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/GBLP_HUMAN GBLP_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. 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:9584165</ref> <ref>PMID:11312657</ref> <ref>PMID:11884618</ref> <ref>PMID:12958311</ref> <ref>PMID:12589061</ref> <ref>PMID:17108144</ref> <ref>PMID:17956333</ref> <ref>PMID:17244529</ref> <ref>PMID:18258429</ref> <ref>PMID:18621736</ref> <ref>PMID:18088317</ref> <ref>PMID:19785988</ref> <ref>PMID:19423701</ref> <ref>PMID:20541605</ref> <ref>PMID:20976005</ref> <ref>PMID:20573744</ref> <ref>PMID:20499158</ref> <ref>PMID:21212275</ref> <ref>PMID:21347310</ref> [[http://www.uniprot.org/uniprot/RL13A_HUMAN RL13A_HUMAN]] Associated with ribosomes but is not required for canonical ribosome function and has extra-ribosomal functions. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma activation and subsequent phosphorylation dissociates from the ribosome and assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation. In the GAIT complex interacts with m7G cap-bound eIF4G at or near the eIF3-binding site and blocks the recruitment of the 43S ribosomal complex. Involved in methylation of rRNA.<ref>PMID:14567916</ref> <ref>PMID:17218275</ref> <ref>PMID:17921318</ref> <ref>PMID:23071094</ref> [[http://www.uniprot.org/uniprot/RS27A_HUMAN RS27A_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref> Ribosomal protein S27a is a component of the 40S subunit of the ribosome.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref> [[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/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/RL11_HUMAN RL11_HUMAN]] Binds to 5S ribosomal RNA (By similarity). Required for rRNA maturation and formation of the 60S ribosomal subunits. Promotes nucleolar location of PML (By similarity).<ref>PMID:19061985</ref> [[http://www.uniprot.org/uniprot/RL7_HUMAN RL7_HUMAN]] Binds to G-rich structures in 28S rRNA and in mRNAs. Plays a regulatory role in the translation apparatus; inhibits cell-free translation of mRNAs. [[http://www.uniprot.org/uniprot/RL6_HUMAN RL6_HUMAN]] Specifically binds to domain C of the Tax-responsive enhancer element in the long terminal repeat of HTLV-I. [[http://www.uniprot.org/uniprot/RL37_HUMAN RL37_HUMAN]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RL35A_HUMAN RL35A_HUMAN]] Required for the proliferation and viability of hematopoietic cells. Plays a role in 60S ribosomal subunit formation. The protein was found to bind to both initiator and elongator tRNAs and consequently was assigned to the P site or P and A site.<ref>PMID:18535205</ref> [[http://www.uniprot.org/uniprot/RL3_HUMAN RL3_HUMAN]] The L3 protein is a component of the large subunit of cytoplasmic ribosomes.
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[https://www.uniprot.org/uniprot/RS8_HUMAN RS8_HUMAN]
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
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<div class="pdbe-citations 4ug0" style="background-color:#fffaf0;"></div>
==See Also==
==See Also==
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*[[Receptor for activated protein kinase C 1|Receptor for activated protein kinase C 1]]
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*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
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*[[3D sructureseceptor for activated protein kinase C 1|3D sructureseceptor for activated protein kinase C 1]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
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</StructureSection>
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</SX>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Khatter, H]]
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[[Category: Large Structures]]
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[[Category: Klaholz, B P]]
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[[Category: Khatter H]]
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[[Category: Myasnikov, A G]]
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[[Category: Klaholz BP]]
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[[Category: Natchiar, S K]]
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[[Category: Myasnikov AG]]
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[[Category: Ribosome]]
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[[Category: Natchiar SK]]

Current revision

STRUCTURE OF THE HUMAN 80S RIBOSOME

4ug0, resolution 3.60Å

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