Ribosomal protein L5

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[[Image:RPL5.png|left|200px|thumb|Crystal Structure of Ribosomal protein L5 from ''Thermus thermophilus'' ([[2xg0]], chain G)]]
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<StructureSection load='1mji' size='350' side='right' caption='Se-Met ribosomal protein L5 complex with 5S RNA from Thermus thermophilus, Mg+2 (green) and K+ (purple) ions (PDB code [[1mji]])' scene=''>
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{{STRUCTURE_2xg0| PDB=2xg0 | SIZE=400| SCENE=Ribosomal_protein_L5/Cv/1 |right|CAPTION=Ribosomal protein L5 from ''Thermus thermophilus'' [[2xg0]], chain G }}
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== Function ==
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[[Ribosomal protein L5]] (RPL5) is one of the 34 proteins which belong to the <scene name='Ribosomal_protein_L5/Cv/2'>large 50S subunit</scene> of the prokaryotic ribosome or to the ca. 49 proteins in the large 60S subunit of the eukaryotic ribosome. It is known to bind to the 5S RRNA from the large subunit. In the archaea like in ''Haloarcula marismortui'', the L5 is called L5P (RPL5P). The 3D structure of the
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Ribosomal protein L5 complex with 5S RNA from Thermus thermophilus, (PDB code [[1mji]]) is shown to the right<ref>PMID:12515387</ref>.
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== Relevance ==
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Mutations in RPL5 are associated with cleft palate and abnormal thumbs in Diamond-Blackfan anemia patients<ref>PMID:19061985</ref>.
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</StructureSection>
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[[Ribosomal protein L5]] (RPL5) is one of the 34 proteins which belong to the <scene name='Ribosomal_protein_L5/Cv/2'>large 50S subunit</scene> of the prokaryotic ribosome or to the ca. 49 proteins in the large 60S subunit of the eukaryotic ribosome. It is known to bind to the 5S RRNA from the large subunit. In the archaea like in ''Haloarcula marismortui'', the L5 is called L5P (RPL5P). The images at the left and at the right correspond to one representative RPL5, ''i.e.'' the crystal structure of Ribosomal protein L5 from ''Thermus thermophilus'' ([[2xg0]], chain G).
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{{TOC limit|limit=2}}
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== 3D Structures of Ribosomal protein L5 ==
== 3D Structures of Ribosomal protein L5 ==
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''Update June 2011''
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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{{#tree:id=OrganizedByTopic|openlevels=0|
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=== RPL5 ===
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[[1iq4]] – RPL5 – ''Geobacillus stearothermophilus''
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=== L5 in 50S subunit+RNA ===
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[[2xg0]], [[2xg2]], [[3kir]], [[3kit]], [[3kiw]], [[3kiy]] – TtRPL5 in 50S subunit+RNA fragments - ''Thermus thermophilus''<br />
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[[2x9s]], [[2x9u]], [[3kni]], [[3knk]], [[3knm]], [[3kno]], [[2wrj]], [[2wrl]], [[2wro]], [[2wrr]], [[3hux]], [[3huz]], [[2wh2]], [[2wh4]], [[2wdi]], [[2wdj]], [[2wdl]], [[2wdn]], [[1vsp]], [[2v47]], [[2v49]], [[1vsa]], [[2hgj]], [[2hgq]], [[2hgu]], [[2j01]], [[2j03]], [[1yl3]], [[3mrz]], [[3ms1]], [[3i8f]], [[3i8i]], [[3i9c]], [[3i9e]], [[3f1f]], [[3f1h]], [[3d5b]], [[3d5d]], [[2b66]], [[2b9n]], [[2b9p]], [[1giy]], [[2y0v]], [[2y0x]], [[2y0z]], [[2y11]], [[2y13]], [[2y15]], [[2y17]], [[2y19]], [[3pyo]], [[3pyr]], [[3pyt]], [[3pyv]] - TtRPL5 in 50S subunit+5S RRNA+23S RRNA<br />
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[[3fin]] - TtRPL5 in 50S subunit+5S RRNA+23S RRNA – Cryo-EM<br />
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[[2wwq]] – EcRPL5 in 50S subunit+5S RRNA+23S RRNA+mRNA+P-site tRNA – ''Escherichia coli''<br />
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[[3i1n]], [[3i1p]], [[3i1r]], [[3i1t]], [[3i20]], [[3i22]], [[3e1b]], [[3e1d]], [[3df2]], [[3df4]], [[2vhn]], [[2qov]], [[2qox]], [[2i2t]], [[2i2v]], [[1vs6]], [[1vs8]], [[2aw4]], [[2awb]], [[3ofd]], [[3og0]], [[1vor]], [[1vou]], [[1vow]], [[1voy]], [[1vp0]], [[1pnu]], [[1pny]], [[3r8s]], [[3r8t]] - EcRPL5 in 50S subunit+5S RRNA+23S RRNA<br />
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[[3fik]], [[2gya]], [[2gyc]], [[3bbx]], [[1p85]], [[1p86]], [[3izt]], [[3izu]] - EcRPL5 in 50S subunit+5S RRNA+23S RRNA – Cryo-EM<br />
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[[3kcr]] - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+preprotein translocase<br />
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[[3j01]] – EcRPL5 in 50S subunit+5S RRNA+23S RRNA+preprotein translocase – Cryo-EM<br />
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[[2rdo]] - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+EF-G+RRF – Cryo-EM<br />
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[[3bbo]] - RPL5 in 50S subunit+5S RRNA+23S RRNA+4.8S RRNA – Cryo-EM – spinach<br />
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[[3iy9]] – RPL5 in 50S subunit – ''Leishmania taretolae''<br />
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[[2zjq]], [[2zjr]], [[1nkw]] - DrRPL5 in 50S subunit+5S RRNA+23S RRNA – ''Deinococcus radiodurans''<br />
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[[1kqs]], [[1qvg]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+CCA - ''Haloarcula marismortui''<br />
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[[1jj2]], [[1ffk]], [[3cc2]], [[2qa4]], [[1s72]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA<br />
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[[3cc7]], [[3cce]], [[3ccj]], [[3ccl]], [[3ccm]], [[3ccq]], [[3ccr]], [[3ccs]], [[3ccu]], [[3ccv]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA (mutant)<br />
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[[1vq4]], [[1vq5]], [[1vq7]], [[1vql]], [[1vqm]], [[1vqp]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+transition state analog<br />
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[[1vq6]], [[1vqk]], [[1vqn]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+ c-hpmn+CCA-Phe-caproic acid-biotin<br />
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[[1vqo]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+ CCPMN<br />
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[[1yhq]], [[1yi2]], [[1yij]], [[1yjn]], [[1yjw]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA (mutant)+antibiotic<br />
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[[1yj9]] - HmRPL5P in 50S subunit (L22 mutant)+5S RRNA+23S RRNA<br />
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[[1qvf]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA + deacylated tRNA minihelix<br />
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[[1q86]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+CCA-Phe-caproic acid-biotin<br />
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=== L5 in 50S subunit + antibiotics ===
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[[3dll]], [[2zjp]], [[3cf5]], [[1xbp]], [[1sm1]], [[1nwx]], [[1nwy]], [[3pio]], [[3pip]] - DrRPL5 in 50S subunit+5S RRNA+23S RRNA+antibiotic <br />
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[[3oh5]], [[3oh7]], [[3ohj]], [[3ohk]], [[3ohz]], [[3oi1]], [[3oi3]], [[3oi5]] – TtRPL5 in 50S subunit+5S RRNA+23S RRNA+antibiotic<br />
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[[2qam]], [[2qao]], [[2qoz]], [[2qp1]], [[2qba]], [[2qbc]], [[3ofc]], [[3ofz]], [[3ofq]], [[3ofr]], [[1vt2]], [[3orb]], [[3oas]], [[3oat]] - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+antibiotic<br />
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[[1k73]], [[1kc8]], [[1k8a]], [[1k9m]], [[1kd1]], [[1m1k]], [[3i55]], [[3i56]], [[3g4s]], [[3g6e]], [[3g71]], [[2qex]], [[3cpw]], [[3cc4]], [[3cd6]], [[2otj]], [[2otl]], [[1yit]], [[1q7y]], [[1q81]], [[1q82]], [[1n8r]], [[1nji]], [[3cxc]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+antibiotics - ''Halobacterium marismortui''<br />
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[[1m90]], [[3cma]], [[3cme]], [[1vq8]], [[1vq9]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+ sparsomycin+CCA-Phe-caproic acid-biotin<br />
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=== L5 in 60S subunit ===
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[[3jyw]] - RPL5 in 60S subunit – ''Thermomyces lanuginosus'' – Cryo-EM<br />
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[[3izr]] - RPL5 in 60S subunit – wheat – Cryo-EM<br />
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[[1s1i]] - yRPL5 in 40S ribosomal subunit+18S RRNA+elongation factor 2 – Cryo-EM – yeast<br />
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3o58, 3o5h – yRPL5 in 60S subunit+25S RRNA+5SRRNA+5.8RRNA
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=== L5 in large + small ribosomal subunit ===
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[[1ml5]] - EcRPL5 in 50S ribosomal subunit+30S ribosomal subunit+THX+chain release factor 2+P-site tRNA+tRNA Phe+mRNA fragment+23S RRNA+5S RRNA+16S RRNA – EM<br />
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[[2zkr]] - RPL5 in 60S ribosomal subunit+30S ribosomal subunit+28S RRNA+5.8S RRNA – Cryo-EM - dog<br />
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=== L5 in 50S subunit + ribosome releasing factor (RRF) ===
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[[2qbe]], [[2qbg]], [[2qbi]], [[2qbk]], [[2z4l]], [[2z4n]] - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+RRF<br />
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=== L5 in 50S subunit + various proteins ===
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[[2vhm]] - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+PDF C-terminal helix<br />
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[[2j28]] - EcRPL5 in 50S subunit+5S RRNA+23S RRNA+signal recognition particle – Cryo-EM<br />
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[[1w2b]] - HmRPL5P in 50S subunit+5S RRNA+23S RRNA+trigger factor N-terminal <br />
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*Ribosomal protein L5
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**[[1iq4]] – RPL5 – ''Geobacillus stearothermophilus''<br />
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**[[5aff]] – RPL5 + RPL11 + symportin – ''Chaetomium thermophilum''<br />
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**[[1mji]] – RPL5 + 5S RRNA – ''Thermus thermophilus''<br />
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**[[5ns3]], [[5ns4]] – TtRPL5 + RNA <br />
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=== L5 in part of 50S subunit ===
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*Ribosomal protein L5 in part of 50S subunit
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[[3iyx]], [[3iyy]] – EcRPL5+RPS13+RPL31 – Cryo-EM<br />
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**[[3iyx]], [[3iyy]] – EcRPL5+RPS13+RPL31 – – ''Escherichia coli'' - Cryo-EM<br />
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[[1mji]] – TtRPL5+5S RRNA
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**[[3j5s]] – EcRPL5+RPL1+RPL33+RPS7+16S RRNA + 23S RRNA + p-site tRNA + ETTA - Cryo-EM<br />
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}}
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== References ==
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<references/>
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[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

Se-Met ribosomal protein L5 complex with 5S RNA from Thermus thermophilus, Mg+2 (green) and K+ (purple) ions (PDB code 1mji)

Drag the structure with the mouse to rotate

3D Structures of Ribosomal protein L5

Updated on 27-February-2022

References

  1. ↑ Perederina A, Nevskaya N, Nikonov O, Nikulin A, Dumas P, Yao M, Tanaka I, Garber M, Gongadze G, Nikonov S. Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex. RNA. 2002 Dec;8(12):1548-57. PMID:12515387
  2. ↑ Gazda HT, Sheen MR, Vlachos A, Choesmel V, O'Donohue MF, Schneider H, Darras N, Hasman C, Sieff CA, Newburger PE, Ball SE, Niewiadomska E, Matysiak M, Zaucha JM, Glader B, Niemeyer C, Meerpohl JJ, Atsidaftos E, Lipton JM, Gleizes PE, Beggs AH. Ribosomal protein L5 and L11 mutations are associated with cleft palate and abnormal thumbs in Diamond-Blackfan anemia patients. Am J Hum Genet. 2008 Dec;83(6):769-80. PMID:19061985 doi:S0002-9297(08)00589-2


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Michal Harel, Alexander Berchansky, Joel L. Sussman

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