View source for 6g53


==Cryo-EM structure of a late human pre-40S ribosomal subunit - State E==
<SX load='6g53' size='340' side='right' viewer='molstar' caption='[[6g53]], [[Resolution|resolution]] 4.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6g53]] is a 37 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=6G53 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6G53 FirstGlance]. <br>
</td></tr><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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6g53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g53 OCA], [http://pdbe.org/6g53 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g53 RCSB], [http://www.ebi.ac.uk/pdbsum/6g53 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g53 ProSAT]</span></td></tr>
</table>
== Disease ==
[[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/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/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/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>  
== Function ==
[[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/NOB1_HUMAN NOB1_HUMAN]] May play a role in mRNA degradation. [[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/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/RS10_HUMAN RS10_HUMAN]] Component of the 40S ribosomal subunit. [[http://www.uniprot.org/uniprot/PNO1_HUMAN PNO1_HUMAN]] Positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA (PubMed:25851604).<ref>PMID:25851604</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/TSR1_HUMAN TSR1_HUMAN]] Required during maturation of the 40S ribosomal subunit in the nucleolus. [[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/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/RS7_HUMAN RS7_HUMAN]] Required for rRNA maturation.<ref>PMID:19061985</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/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>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage.

Visualizing late states of human 40S ribosomal subunit maturation.,Ameismeier M, Cheng J, Berninghausen O, Beckmann R Nature. 2018 Jun 6. pii: 10.1038/s41586-018-0193-0. doi:, 10.1038/s41586-018-0193-0. PMID:29875412<ref>PMID:29875412</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6g53" style="background-color:#fffaf0;"></div>

==See Also==
*[[Receptor for activated protein kinase C 1|Receptor for activated protein kinase C 1]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
<references/>
__TOC__
</SX>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Ameismeier, M]]
[[Category: Beckmann, R]]
[[Category: Berninghausen, O]]
[[Category: Cheng, J]]
[[Category: Pre-40]]
[[Category: Ribosome]]
[[Category: Ribosome biogenesis]]