Ribosome 3D structures: Difference between revisions

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**[[6fyx]], [[6fyy]] – y48S + IF-5 - Cryo_EM<br />
**[[6fyx]], [[6fyy]] – y48S + IF-5 - Cryo_EM<br />


*50S subunit
*50S subunit


**[[2ftc]] – b50S subunit – bovine - Cryo_EM<br />
**[[2ftc]] – b50S subunit – bovine - Cryo_EM<br />
Line 133: Line 133:
**[[5zet]], [[6dzp]], [[5o60]], [[5xym]] – Ms50S ribosomal subunit - Cryo EM<br />
**[[5zet]], [[6dzp]], [[5o60]], [[5xym]] – Ms50S ribosomal subunit - Cryo EM<br />


*50S subunit + antibiotics
*50S subunit + antibiotics


**[[3dll]], [[2zjp]], [[3cf5]], [[1xbp]], [[1sm1]], [[1nwx]], [[1nwy]], [[3pio]], [[3pip]] - Dr50S subunit +general stress protein Ctc+ antibiotic<br />  
**[[3dll]], [[2zjp]], [[3cf5]], [[1xbp]], [[1sm1]], [[1nwx]], [[1nwy]], [[3pio]], [[3pip]] - Dr50S subunit +general stress protein Ctc+ antibiotic<br />  
 
**[[4io9]], [[4ioa]], [[4ioc]] - Dr50S subunit + antibiotics<br />
[[4io9]], [[4ioa]], [[4ioc]] - Dr50S subunit + antibiotics<br />
**[[6u48]] - Ec50S subunit + antibiotics<br />
**[[6u48]] - Ec50S subunit + antibiotics<br />
**[[6qul]] - Ec50S subunit + P-site tRNA-fMet + antibiotics<br />
**[[6qul]] - Ec50S subunit + P-site tRNA-fMet + antibiotics<br />
Line 145: Line 144:
**[[5v7q]] – Mt50S subunit + antibiotic – ''Mycobacterium tuberculosis'' – Cryo EM<br />
**[[5v7q]] – Mt50S subunit + antibiotic – ''Mycobacterium tuberculosis'' – Cryo EM<br />


*50S subunit + ribosome releasing factor (RRF)
*50S subunit + ribosome releasing factor (RRF)


**[[2rdo]] - Ec50S subunit +EF-G+RRF – Cryo-EM<br />
**[[2rdo]] - Ec50S subunit +EF-G+RRF – Cryo-EM<br />
**[[3j0d]] - Tt50S subunit+RRF – Cryo-EM<br />
**[[3j0d]] - Tt50S subunit+RRF – Cryo-EM<br />


*50S subunit + various proteins
*50S subunit + various proteins


**[[2j28]] - Ec50S subunit +signal recognition particle – Cryo-EM<br />
**[[2j28]] - Ec50S subunit +signal recognition particle – Cryo-EM<br />
Line 159: Line 158:
**[[1w2b]] - Hm50S subunit +trigger factor N-terminal<br />
**[[1w2b]] - Hm50S subunit +trigger factor N-terminal<br />
**[[1qvf]]- Hm50S subunit + deacylated tRNA minihelix<br />
**[[1qvf]]- Hm50S subunit + deacylated tRNA minihelix<br />
**[1q86]] - Hm50S subunit +CCA-Phe-caproic acid-biotin<br />
**[[1q86]] - Hm50S subunit +CCA-Phe-caproic acid-biotin<br />
**[[3cma]], [[3cme]], [[1vq8]], [[1vq9]], [[1m90]] - Hm50S subunit +CCA+CCA-Phe-CAP-BIO<br />
**[[3cma]], [[3cme]], [[1vq8]], [[1vq9]], [[1m90]] - Hm50S subunit +CCA+CCA-Phe-CAP-BIO<br />
**[[1vq4]], [[1vq5]], [[1vq7]], [[1vql]], [[1vqm]], [[1vqp]] – Hm50S subunit +transition state analog<br />
**[[1vq4]], [[1vq5]], [[1vq7]], [[1vql]], [[1vqm]], [[1vqp]] – Hm50S subunit +transition state analog<br />

Revision as of 12:18, 30 December 2019

Updated on 30-December-2019 For a general description of the protein see Ribosome

{{#tree:id=OrganizedByTopic|openlevels=0|

  • 30S subunit + RNA

1i94, 1fka, 4dr1 - Tt30S ribosomal subunit+16S rRNA

  • 30S subunit +tRNA+mRNA
    • 3t1h, 3t1y - Tt30S ribosomal subunit+16S rRNA+tRNA Lys +mRNA
    • 6dti, 6mkn - Tt30S ribosomal subunit+16S rRNA+tRNA Arg +mRNA
    • 3v6u, 3v6v - Tt30S ribosomal subunit+16S rRNA+tRNA Phe+tRNA fMet+mRNA
    • 1xnq, 1xnr - Tt30S ribosomal subunit+THX+mRNA+tRNA anticodon+16S rRNA
    • 4gkj, 4gkk - Tt30S ribosomal subunit +16S rRNA +THX + mRNA + tRNA Met
    • 4jv5, 4jya, 4k0k - Tt30S ribosomal subunit +16S rRNA +THX + mRNA + ASL-tRNA
  • 30S subunit +A-site tRNA
    • 2uxd, 2uxc - Tt30S ribosomal subunit+THX+A-site mRNA CGGG+tRNA anticodon+16S rRNA
    • 1n32, 1n33 - Tt30S ribosomal subunit+THX+A-site mRNA fragment+tRNA anticodon+16S rRNA
    • 1n34 - Tt30S ribosomal subunit+THX+A-site mRNA fragment +16S rRNA
    • 1xmo, 1xmq - Tt30S ribosomal subunit+THX+A-site mRNA+tRNA anticodon+16S rRNA
    • 2uxb - Tt30S ribosomal subunit+THX+A-site mRNA GGGU+tRNA anticodon+16S rRNA
  • 30S subunit+P-site tRNA
    • 1ibk - Tt30S ribosomal subunit+THX+P-site mRNA fragment +16S rRNA
    • 2om7 – TtRPS2+TtRPS12+TtRPL1+ P-site tRNA+16S rRNA fragment+23S RRNA fragment
    • 5u4j – EcRPS3+EcRPS4+EcRPS5 + EcRPS12 + P-site tRNA+16S rRNA +23S rRNA + mRNA + RF-2 – Cryo EM
    • 5zeu - Ms30S ribosomal subunit + P-site tRNA f`Met +16S rRNA - Cryo EM
  • 30S subunit+A-site tRNA+P-site tRNA
    • 1ibl, 1ibm - Tt30S ribosomal subunit+THX+A-site mRNA fragment+P-site mRNA fragment+tRNA anticodon+16S rRNA


  • 30S subunit+A-site tRNA+P-site tRNA+E-site tRNA
    • 1jgo, 1jgp, 1jgq - Tt30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+tRNA Phe+mRNA +16S rRNA
  • 30S subunit + antibiotics


  • 30S subunit + ribosome recycling factor
    • 3r8n, 3r8o - Ec30S ribosomal subunit+16S rRNA+ribosome recycling factor + mRNA + tRNA
  • 30S subunit + elongation factor
    • 4btc - Tt30S ribosomal subunit+THX+RNA +16S rRNA+elongation factor G
    • 6enu - Ec30S ribosomal subunit+THX+RNA +16S rRNA+elongation factor P – Cryo EM
  • 30S subunit + translation initiation factor
    • 1hr0 - Tt30S ribosomal subunit+THX+IF+16S rRNA
    • 1i96 - Tt30S ribosomal subunit+THX+IF3+16S rRNA
    • 6o7k - Ec30S ribosomal subunit+THX+IF1 + IF2 +16S rRNA - tRNA + mRNA – Cryo EM
  • 30S subunit + various proteins
    • 1x18 – TtRPS2+TtRPS7+TtRPS11+TtRPS18+GTP-binding protein ERA+RNA fragments
    • 6ny6 - Tt30S ribosomal subunit + toxin YoeB
    • 2ykr - EcRPS2 + 16S rRNA + GMPPNP + GTPase RSGA
    • 4a2i - EcRPS2 + 16S rRNA + GTPase RSGA – Cryo EM
    • 4adv - EcRPS2 + 16S rRNA + methyltransferase – Cryo EM
    • 5uz4, 5no3, 5no2 - Ec30S ribosomal subunit+ BS6 + US7 + GTPase RsgA +16S rRNA – Cryo EM
    • 6awb, 6awc, 6awd - Ec30S ribosomal subunit + RNA polymerase - Cryo EM
    • 6dzk - Ms30S ribosomal subunit + HPF +16S rRNA - Cryo EM
  • 40S ribosomal subunit
  • 40S ribosomal subunit complex
    • 6nf8, 6neq - h40S ribosomal subunit + translation initiation factor 3 - Cryo-EM
    • 5oa3 - h40S ribosomal subunit + translation initiation factor 2D - Cryo-EM
    • 6g4w - h40S ribosomal subunit + PNO1 + bystin + TSR1 + tRNA methyltransferase - Cryo-EM
    • 6g5h - h40S ribosomal subunit + RACK1 - Cryo-EM
    • 5vyc - h40S ribosomal subunit + DENR-MCT-1 - Cryo-EM
    • 4kzx - r40S ribosomal subunit+ RACK1 + EIF1 – rabbit – Cryo-EM
    • 4kzy - r40S ribosomal subunit+ RACK1 + EIF1 + EIF1A – Cryo-EM
    • 4kzz - r40S ribosomal subunit+ RACK1 + EIF1A + initiator tRNA – Cryo-EM
    • 6p4g, 6p4h - r40S ribosomal subunit + IRES virus – Cryo-EM
    • 4bts - r40S ribosomal subunit+ 18SrRNA + EIF1 + EIF1A
    • 6fai - y40S ribosomal subunit + PNO1 + 20S rRNA + TSR1 + LTV1 + RIO2 - Cryo-EM
    • 6eml - y40S ribosomal subunit + PNO1 + 20S rRNA + TSR1 + LTV1 + RIO2 + essential nuclear protein 1 – Cryo-EM
    • 6rbe, 6rbd - y40S ribosomal subunit + TSR1 – Cryo-EM
    • 6nd4 - y40S ribosomal subunit + SOF1 + IMP3 + MPP10 + BUD21 + NOP56 + NOP58 + NOP1 + SNU13 + RRP9 + FAF1 – Cryo-EM
    • 4v5o - Tet40S ribosomal subunit+RACK1 – Tetrahymena thermophila
    • 5xyi - Tv40S ribosomal subunit+ RACK1 – Trichomonas vaginalis - Cryo-EM
    • 5opt – Tc40S ribosomal subunit + KSRP – Trypanosoma cruzi - Cryo-EM
    • 6okk – Pf40S ribosomal subunit + antibiotics – Plasmodium falciparum - Cryo-EM
  • 48S preinitiation
  • 50S subunit
  • 50S subunit + antibiotics
  • 50S subunit + ribosome releasing factor (RRF)
    • 2rdo - Ec50S subunit +EF-G+RRF – Cryo-EM
    • 3j0d - Tt50S subunit+RRF – Cryo-EM
  • 50S subunit + various proteins
    • 2j28 - Ec50S subunit +signal recognition particle – Cryo-EM
    • 6i0y - Ec50S subunit + tRNA – Cryo-EM
    • 6s0k - Ec50S subunit + tRNA + SecA + RodZ – Cryo-EM
    • 5o2r - Ec50S subunit + antimicrobial peptide – Cryo-EM
    • 5ot7 - Ec50S subunit + EF-G – Cryo-EM
    • 1w2b - Hm50S subunit +trigger factor N-terminal
    • 1qvf- Hm50S subunit + deacylated tRNA minihelix
    • 1q86 - Hm50S subunit +CCA-Phe-caproic acid-biotin
    • 3cma, 3cme, 1vq8, 1vq9, 1m90 - Hm50S subunit +CCA+CCA-Phe-CAP-BIO
    • 1vq4, 1vq5, 1vq7, 1vql, 1vqm, 1vqp – Hm50S subunit +transition state analog
    • 1vq6, 1vqk, 1vqn – Hm50S subunit + c-hpmn+CCA-Phe-caproic acid-biotin
    • 1vqo – Hm50S subunt + CCPMN
    • 6ppk - Bs50S subunit + ribosome biogenesis GTPase A – Cryo EM
    • 6ha8 - Bs50S subunit + VmlR – Cryo EM
    • 6htq - Bs50S subunit + RelA – Cryo EM
    • 6szs - Bs50S subunit + BrfA – Cryo EM
  • 60S subunit
  • 60S subunit + various proteins
    • 3j3b – h60S subunit + P0 + P1 + P2 - Cryo EM
    • 3izs – y60S subunit + P0 + P1 + P2 - Cryo EM
    • 4v8t – y60S subunit + P0 + P1 + P2 + ARX1 - Cryo EM
    • 3o5h – y60S subunit + 5S rRNA + 5.8S rRNA + 25S rRNA + P0
    • 6em5, 6em4, 6em3, 6elz, 6em1 – y60S ribosomal subunit + BRX1 + 5.8S rRNA + 25S RNA + CIC1 + ERB1 + HAS1 + MRT4 + NIP7 + ribosome biogenesis proteins + EIF-6 + nucleolar proteins – Cryo-EM
    • 6cb1, 6c0f, 5z3g – y60S ribosomal subunit + 5.8S rRNA + 25S RNA + CIC1 + HAS1 + MRT4 + NIP7 + ribosome biogenesis proteins + RNA-processing protein + nucleolar proteins + pescadillo homolog – Cryo-EM
    • 6r87, 6r84 – y60S subunit + Vms1 – Cryo EM
    • 5t6r, 5t62 – y60S subunit + Nmd3 – Cryo EM
    • 6ft6 – y60S ribosomal subunit + NOP53 – Cryo-EM
    • 5anc, 5anb, 5an9 – sm60S subunit + P0 + SbdS + EF-Tu – slime mold - Cryo EM
    • 6qkl – sm60S subunit + P0 + SbdS + EIF-6 - Cryo EM
    • 3j39 – Dm60S subunit + P0 – Drosophila melanogaster - Cryo EM
    • 4v8p - Tet60S subunit+ 26S rRNA+ translation initiation factor 6
  • 70S ribosome
  • 70S ribosome complex with mRNA
  • 70S ribosome complex with antibiotic
  • 70S ribosome complex with release factor
    • 6eri – sRibosome + RRF + hibernation promoting factor - Cryo-EM
    • 4v5a – TtRibosome + RRF
    • 4v63, 4v7p, 6bok – TtRibosome + RF-1
    • 4v5e, 4v4r, 4v67, 4v9n – TtRibosome + RF-2
    • 4v5j – TtRibosome + RF-2 + substrate analog
    • 4v8o – TtRibosome + RF-3
    • 4v54 – EcRibosome + RRF
    • 6dnc, 6osk, 6osq – EcRibosome + RF-1 – Cryo-EM
    • 6ouo, 6og7, 6ogf, 6ogg, 6ogi, 6ot3, 6ost – EcRibosome + RF-2 – Cryo-EM
    • 5u4i, 5u9f, 5u9g – EcRibosome + RF-2 + ArfA – Cryo-EM
    • 4v89 – EcRibosome + RF-3
    • 6gxp – EcRibosome + RF-3 – Cryo EM
    • 4v85 – EcRibosome + RF-3 + mRNA + antibiotic
    • 6gwt, 6gxm, 6gxn, 6gxo – EcRibosome + RF-1+ RF-3 + P-site tRNA – Cryo-EM
  • 70S ribosome complex with various proteins
    • 4v5b – EcRibosome + PDF-binding helix
    • 4v5h – EcRibosome + Tnac leader peptide
    • 4v6v - EcRibosome+ tetracycline resistance protein + mRNA + P-tRNA – Cryo-EM
    • 4v6m – EcRibosome + SecYE – Cryo-EM
    • 4v4g – EcRibosome + protein Y – Cryo-EM
    • 5wdt, 5we4 – EcRibosome + EF-Tu – Cryo-EM
    • 5we6 – EcRibosome + EF-Tu + tRNA + GTP – Cryo-EM
    • 6enj – EcRibosome + EF-P + A-site tRNA + P-site tRNA – Cryo-EM
    • 4v7i – EcRibosome +preprotein translocase – Cryo-EM
    • 4v49 - EcRibosome +general stress protein Ctc – Cryo-EM
    • 4v8g, 4v8h – TtRibosome + modulation factor
    • 4v8i - TtRibosome + ribosome-associated inhibitor
    • 4v95 – TtRibosome + YAEJ
    • 4v5k – TtRibosome + colicin E3
    • 4v7j, 4v7k – TtRibosome + toxin RelE
    • 6otr, 6oxa, 6oxi - TtRibosome + toxin YoeB
    • 6cfk – TtRibosome + His-CAM + YfiA
    • 6cfl – TtRibosome + Lys-CAM + YfiA
    • 6fkr – TtRibosome + Tur1A
    • 5zlu – TtRibosome + ABC-F – Cryo-EM
    • 6dzi – MsRibosome + MPY – Cryo-EM
  • 70S ribosome complex with tRNA mRNA
    • 6gsj, 6gsk, 6gsl – TtRibosome + A-site tRNA-Thr + mRNA + tRNA-fMet
    • 6n1d – TtRibosome + mRNA + tRNA
    • 6bz7, 6bz8 – TtRibosome + A-site tRNA-Leu
    • 5vpo, 5vpp, 6ndk – TtRibosome + tRNA-SufA6
    • 6n9e, 6n9f – TtRibosome + mRNA + P-site tRNA
    • 6uo1 – TtRibosome + mRNA + A-site tRNA + P-site tRNA + E-site tRNA
    • 6q95, 6q97 – TtRibosome + A-site tRNA – Cryo-EM
    • 6q98 – TtRibosome + P-site tRNA – Cryo-EM
    • 6q9a – TtRibosome + E-site tRNA – Cryo-EM
    • 5uq7 – TtRibosome + A-site tRNA + dnaX – Cryo-EM
    • 5uq8 – TtRibosome + E-site tRNA + dnaX – Cryo-EM
    • 6cfj – TtRibosome + His-CAM + A-site tRNA + P-site tRA + E-site tRNA + mRNA + antibiotic
  • 70S ribosome complex with elongation factor
    • 4v9o – EcRibosome + EF-G
    • 4v9p – EcRibosome + antibiotic + EF-G
    • 4v47 – EcRibosome + elongation factor G – Cryo-EM
    • 4v6t – EcRibosome + EF-G + tRNA-SmpB – Cryo-EM
    • 4v6k, 4v6l – EcRibosome + EF-Tu
    • 4v5l – EcRibosome + EF-Tu + tRNA
    • 5wfk, 5wf0, 5wfs – EcRibosome + EF-Tu + tRNA – Cryo EM
    • 4v5f, 4v8u, 4v9h – TtRibosome + EF-G
    • [[4v56a] – TtRibosome + EF-P
    • 4v5g – TtRibosome + EF-Tu
    • 4v8q – TtRibosome + antibiotic + EF-Tu
    • 4v68 – TtRibosome + antibiotic + EF-Tu – Cryo-EM
    • 4v5p, 4v5q, 4v5r, 4v5s – TtRibosome + EF-Tu + tRNA-Trp
    • 4v9j, 4v9k, 4v9l, 4v9m – TtRibosome + -EF-G + tRNA
    • 4v9l – TtRibosome + EF-G + antibiotic + tRNA
  • 80S ribosome
  • 80S ribosome complexes
    • 6r6p – hRibosome + XBP1u - Cryo-EM
    • 6olg, 6oli – hRibosome + drug - Cryo-EM
    • 6olz – hRibosome + tRNA + drug - Cryo-EM
    • 6ole, 6olf, 6om0, 6om7 – hRibosome + A-site tRNA + P-site tRNA + drug - Cryo-EM
    • 6fti, 6ftj - dRibosome + oligosaccharyltransferase + Sec61 - Cryo-EM
    • 6ftg - dRibosome + OST - Cryo-EM
    • 3j0l, 3j0o, 3j0p, 3j0q - rRibosome+ mRNA – Cryo-EM
    • 6mte, 6mtd – rRibosome + EF2 + SERBP1 - Cryo-EM
    • 6d9j, 6d90 – rRibosome + RF-1 + P-site tRNA - Cryo-EM
    • 6frk – rRibosome + SRP + SRP receptor - Cryo-EM
    • 6hcj – rRibosome + A-site tRNA + P-site tRNA - Cryo-EM
    • 6mtb – rRibosome + P-site tRNA + Z-site tRNA - Cryo-EM
    • 6mtc – rRibosome + Z-site tRNA + IFRD2 - Cryo-EM
    • 6r5q – rRibosome + XBP1u - Cryo-EM
    • 6r6g – rRibosome + XBP1u + SRP - Cryo-EM
    • 6r7q – rRibosome + XBP1u + Sec61 - Cryo-EM
    • 6t59 – rRibosome +b-tubulin- Cryo-EM
    • 6p5i, 6p5j, 6p5k, 6p5n, 6ip6, 6ip8 - rRibosome + IRES virus – Cryo-EM
    • 4v6w - DmRibosome + EF2 + guanine nucleotide-binding protein – Cryo-EM
    • 4v4b – yRibosome + EF2 + antifungal - Cryo-EM
    • 6gqv, 6gqb, 6gq1 – yRibosome + EF2 + mRNA + tRNA - Cryo-EM
    • 5tga, 5tgm – yRibosome + A-site tRNA-Pro
    • 5tbw, 5obm, 5on6 – yRibosome + antibiotic
    • 6hd7 – yRibosome + NatA – Cryo EM
    • 6s47 – yRibosome + New1 – Cryo EM
    • 6hhq – yRibosome + C45 – Cryo EM
    • 6q8y – yRibosome + Xrn1 – Cryo EM
    • 4v7h - TlRibosome+P-site tRNA – Thermomyces lanuginosus
    • 5umd – PfRibosome + mefloquin - Cryo-EM
    • 5osg – LdRibosome + KSRP - Cryo-EM
  • 90S pre-ribosome
  • 100S ribosome
  • Mitoribosome
  • 28S subunit
    • 6gaz – p28S ribosomal subunit – pig - Cryo-EM
    • 3jd5 – b28S ribosomal subunit - Cryo-EM
    • 6sg9, 6sga, 6sgb – Tb28S ribosomal subunit - Cryo-EM
    • 6hiy, 6hiw – Tb28S ribosomal subunit+ IF-3 - Cryo-EM
  • 39S subunit
    • 5oom – h39S ribosomal subunit - Cryo-EM
    • 5ool – h39S ribosomal subunit + rRNA - Cryo-EM
    • 6gb2, 4v19, 4v1a – p39S ribosomal subunit - Cryo-EM
    • 6hix – Tb39S ribosomal subunit - Cryo-EM
  • 55S mitoribosome
    • 6nu2, 6nu3 – h55S subunit + RRF - Cryo EM
    • 6gaw, 5aj4, 5aj3 – p55S ribosome - Cryo-EM
    • 6hiv – Tb55S ribosome - Cryo-EM

}}

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Jaime Prilusky, Alexander Berchansky, Wayne Decatur, Michal Harel, Joel L. Sussman
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