Ribosome 3D structures: Difference between revisions

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**[[3bbn]] - 30S ribosomal subunit+16S RRNA – Cryo-EM – spinach<br />
**[[3bbn]] - 30S ribosomal subunit+16S RRNA – Cryo-EM – spinach<br />


* 30S subunit + chain release factor
*30S subunit + chain release factor


**[[3mr8]], [[3ms0]] – Tt30S ribosomal subunit+THX+chain release factor 1+P-site tRNA+mRNA+16S RRNA <br />
**[[3mr8]], [[3ms0]] – Tt30S ribosomal subunit+THX+chain release factor 1+P-site tRNA+mRNA+16S RRNA <br />
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**[[3j3v]], [[3j3w]] - 50S subunit+5S RRNA+23S RRNA – ''Bacillus subtilis''<br />
**[[3j3v]], [[3j3w]] - 50S subunit+5S RRNA+23S RRNA – ''Bacillus subtilis''<br />


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


**[[3dll]], [[2zjp]], [[3cf5]], [[1xbp]], [[1sm1]], [[1nwx]], [[1nwy]], [[3pio]], [[3pip]] - Dr50S subunit+5S RRNA+23S RRNA+general stress protein Ctc+ antibiotic<br />  
**[[3dll]], [[2zjp]], [[3cf5]], [[1xbp]], [[1sm1]], [[1nwx]], [[1nwy]], [[3pio]], [[3pip]] - Dr50S subunit+5S RRNA+23S RRNA+general stress protein Ctc+ antibiotic<br />  
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**[[3zf7]] - Tb60S subunit - Cryo EM<br />
**[[3zf7]] - Tb60S subunit - Cryo EM<br />


* large + small ribosomal subunit
*large + small ribosomal subunit


**[[1ml5]] - Ec50S ribosomal subunit+30S ribosomal subunit+THX+chain release factor 2+P-site tRNA+tRNA Phe+mRNA fragment+23S RRNA+5S RRNA+16S RRNA – Cryo-EM<br />
**[[1ml5]] - Ec50S ribosomal subunit+30S ribosomal subunit+THX+chain release factor 2+P-site tRNA+tRNA Phe+mRNA fragment+23S RRNA+5S RRNA+16S RRNA – Cryo-EM<br />
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**[[4u3m]], [[4u56]], [[4u3n]], [[4u55]], [[4u3u]], [[4u53]], [[4u4n]], [[4u4o]], [[4u4q]], [[4u4r]], [[4u4u]], [[4u52]], [[4u51]], [[4u4y]], [[4u4z]], [[4u6f]], [[4u50]] - y60S ribosomal subunit+40S ribosomal subunit in complexes with 12 eukaryote-specific and 4 broad-spectrum inhibitors
**[[4u3m]], [[4u56]], [[4u3n]], [[4u55]], [[4u3u]], [[4u53]], [[4u4n]], [[4u4o]], [[4u4q]], [[4u4r]], [[4u4u]], [[4u52]], [[4u51]], [[4u4y]], [[4u4z]], [[4u6f]], [[4u50]] - y60S ribosomal subunit+40S ribosomal subunit in complexes with 12 eukaryote-specific and 4 broad-spectrum inhibitors


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


**[[2rdo]] - Ec50S subunit+5S RRNA+23S RRNA+EF-G+RRF – Cryo-EM<br />
**[[2rdo]] - Ec50S subunit+5S RRNA+23S RRNA+EF-G+RRF – Cryo-EM<br />
**[[3j0d]] - Tt50S subunit+5S RRNA+23S RRNA+RRF – Cryo-EM<br />
**[[3j0d]] - Tt50S subunit+5S RRNA+23S RRNA+RRF – Cryo-EM<br />


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


**[[2vhm]] - Ec50S subunit+5S RRNA+23S RRNA+PDF C-terminal helix<br />
**[[2vhm]] - Ec50S subunit+5S RRNA+23S RRNA+PDF C-terminal helix<br />

Revision as of 17:01, 12 June 2015

Updated on 12-June-2015 For a general description of the protein see Ribosome

    • 1ibl, 1ibm - Tt30S ribosomal subunit+THX+A-site mRNA fragment+P-site mRNA fragment+tRNA anticodon+16S RRNA
  • 30S subunit+P-site tRNA+E-site tRNA
    • 2ow8 - Tt30S ribosomal subunit+THX+P-site tRNA Phe+E-site tRNA+mRNA +16S RRNA
    • 2b9o - Tt30S ribosomal subunit+THX+P-site tRNA Phe+E-site tRNA Phe+mRNA +16S RRNA
    • 2qnh - Tt30S ribosomal subunit+THX+P-site tRNA+E-site tRNA+mRNA +16S RRNA
    • 2wdg, 2wdh, 2wdk, 2wdm - Tt30S ribosomal subunit+THX+P-site tRNA+E-site tRNA+mRNA +16S RRNA+tRNA Phe
  • 30S subunit+A-site tRNA+P-site tRNA+E-site tRNA
    • 2gy9, 2gyb - Ec30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+mRNA +16S RRNA – Cryo-EM
    • 1jgo, 1jgp, 1jgq, 1gix - Tt30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+tRNA Phe+mRNA +16S RRNA
    • 3e1a, 3e1c - Ec30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+mRNA +16S RRNA
  • 30S subunit + antibiotics
  • 30S subunit + ribosome recycling factor
    • 2qbd, 2qbf -Ec30S ribosomal subunit+16S RRNA+ribosome recycling factor
    • 3r8n, 3r8o, 4gd1, 4gd2 - Ec30S ribosomal subunit+16S RRNA+ribosome recycling factor + mRNA + tRNA
    • 2qbh, 2qbj - Ec30S ribosomal subunit+16S RRNA+ribosome recycling factor+gentamicin
    • 2v46, 2v48 - Tt30S ribosomal subunit+16S RRNA+ribosome recycling factor+P-site tRNA Phe+mRNA+tRNA fMet
  • 30S subunit + elongation factor
    • 2wri, 2wrk - Tt30S ribosomal subunit+THX+P-site tRNA+mRNA +16S RRNA+elongation factor G
    • 2wrn, 2wrq - Tt30S ribosomal subunit+THX+A-site tRNA+mRNA +16S RRNA+elongation factor TU-4
    • 3fic - Tt30S ribosomal subunit+THX+A-site tRNA+P-site tRNA+E-site tRNA+mRNA codon+16S RRNA+elongation factor TU-A
    • 4abr - Tt30S ribosomal subunit+THX + E/P-site tRNA fMet +mRNA codon+16S RRNA+elongation factor TU
    • 2y0u, 2y0w, 2y0y, 2y12, 2y10, 2y18, 2y14, 2y16 - Tt30S ribosomal subunit+THX+A-site tRNA+E-site tRNA+mRNA codon+16S RRNA+elongation factor TU
    • 3fih - Ec30S ribosomal subunit+A-site tRNA Phe+P-site tRNA+mRNA +16S RRNA+elongation factor TU
    • 3izv - Ec30S ribosomal subunit+A/T-site tRNA Phe +16S RRNA+elongation factor TU
    • 3j18 - Ec30S ribosomal subunit+A/T-site tRNA Phe +16S RRNA+ mRNA + SSRA-binding protein + formyl-Met specific initiator tRNA + elongation factor G – Cryo-EM
    • 3izw - Ec30S ribosomal subunit+A-site tRNA Phe +mRNA +16S RRNA+elongation factor TU
    • 3huw, 3huy - Tt30S ribosomal subunit+THX+tRNA-Met+mRNA +16S RRNA+elongation factor P
    • 4b8f, 4b8h - Tt30S ribosomal subunit+THX+RNA+mRNA +16S RRNA+elongation factor G
    • 4btc, 4kdg, 4kdj - Tt30S ribosomal subunit+THX+RNA +16S RRNA+elongation factor G
    • 4juw - Tt30S ribosomal subunit+THX+ tRNA Phe +16S RRNA + mRNA +elongation factor G
    • 4kbt, 4kbv, 4kcy, 4kd0, 4kd8, 4kda - Tt30S ribosomal subunit+THX+ tRNA Met +16S RRNA + mRNA + viomycin + elongation factor G
    • 4kiy, 4kj0, 4kj2, 4kj4, 4kj6, 4kj8, 4kja, 4kjc - Ec30S ribosomal subunit +16S RRNA + viomycin + elongation factor G
  • 30S subunit + translation initiation factor
    • 1hr0 - Tt30S ribosomal subunit+THX+IF+16S RRNA
    • 1i96 - Tt30S ribosomal subunit+THX+IF3+16S RRNA
  • 30S subunit + various proteins
    • 3kiq, 3kis, 3kiu, 3kix - Tt30S ribosomal subunit+toxin RelE+16S RRNA
    • 2xfz, 2xg1 - Tt30S ribosomal subunit+colicin-E3 fragment+16S RRNA+mRNA+E-site tRNA+THX
    • 1voq, 1vos , 1vov, 1vox, 1voz - Ec30S ribosomal subunit+protein Y+16S RRNA
    • 3j36 - Ec30S ribosomal subunit+ tetracycline resistance protein +16S RRNA + mRNA + P-tRNA – Cryo-EM
    • 1x18 – TtRPS2+TtRPS7+TtRPS11+TtRPS18+GTP-binding protein ERA+RNA fragments
    • 4dh9, 4dhb - Tt30S ribosomal subunit +16S RRNA+mRNA+P-site tRNA fMet +THX + YAEJ
    • 3v22, 3v24, 3v26, 3v28 - Tt30S ribosomal subunit +16S RRNA +THX + modulation factor
    • 3v2c, 3v2e - Tt30S ribosomal subunit +16S RRNA +THX + ribosome-associated inhibitor
    • 3j00 – EcRPS2 + 16S RRNA + FTSQ + apolipoprotein A-I
    • 2ykr - EcRPS2 + 16S RRNA + GMPPNP + GTPase RSGA
    • 4a2i - EcRPS2 + 16S RRNA + GTPase RSGA – Cryo EM
    • 3uoq - EcRPS2 + 16S RRNA + mRNA + peptide chain release factor
    • 4adv - EcRPS2 + 16S RRNA + methyltransferase – Cryo EM
  • 40S ribosomal subunit
    • 3jyv - Tl40S ribosomal subunit+RACK1+S19E+P-site tRNA – Thermomyces lanuginosus
    • 2xzm, 2xzn - Tet40S ribosomal subunit+RACK1 – Tetrahymena thermophila
    • 1s1h - y40S ribosomal subunit+18S RRNA+elongation factor 2 – Cryo-EM – yeast
    • 3izb - y40S ribosomal subunit+ RACK1 – Cryo-EM
    • 3o2z, 3o30 - y40S ribosomal subunit+ RACK1
    • 3u5c, 3u5g - y40S ribosomal subunit+ RACK1 + suppressor protein SMT1
    • 3iz6 - w40S ribosomal subunit+RACK1 – wheat
    • 3j38 - Dm40S ribosomal subunit + EF-2 + guanine nucleotide-binding protein – Drosophila melanogaster – Cryo-EM
    • 3j3a - h40S ribosomal subunit + EF-2 + guanine nucleotide-binding protein – human – 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
    • 2zkq – d40S ribosomal subunit+RACK1+RRNA fragment – dog - Cryo-EM
    • 3zey - Tb40S ribosomal subunit – Trypanosoma brucei – Cryo-EM
    • 4bpe, 4bpn, 4bpo, 4bpp - r40S ribosomal subunit+ 18SRRNA + EIF1 + EIF1A
  • 50S subunit+RNA
  • 50S subunit + antibiotics
  • 60S subunit
    • 3jyw - 60S subunit – Thermomyces lanuginosus – Cryo-EM
    • 1s1i, 1s1h - y60S ribosomal subunit+ 5.8S RRNA+ 5S RRNA – Cryo-EM
    • 3izs - y60S subunit – Cryo-EM
    • 3u5e, 3u5i - y60S subunit
    • 3o58, 3o5h - y60S ribosomal subunit+ 5.8S RRNA+ 5S RRNA + 25S RRNA
    • 3izr, 3izt, 3izu, 3izs - w60S subunit
    • 3j39 – Dm60S subunit – Cryo-EM
    • 3j3b – h60S subunit – Cryo-EM
    • 4a17, 4a1a, 4a1c, 4a1e - Tet60S ribosomal subunit + 5S RRNA + 5.8S RRNA
    • 3zf7 - Tb60S subunit - Cryo EM
  • large + small ribosomal subunit
    • 1ml5 - Ec50S ribosomal subunit+30S ribosomal subunit+THX+chain release factor 2+P-site tRNA+tRNA Phe+mRNA fragment+23S RRNA+5S RRNA+16S RRNA – Cryo-EM
    • 2qan, 2qal, 2qou, 2qow, 2qoy, 2qp0 - Ec50S ribosomal subunit+30S ribosomal subunit
    • 2zkr - d60S ribosomal subunit+30S ribosomal subunit+28S RRNA+5.8S RRNA – dog - Cryo-EM
    • 3j0l - r60S ribosomal subunit+40S ribosomal subunit+RRNA fragments+ mRNA fragments – rabbit - Cryo-EM
    • 3j0o, 3j0p, 3j0q - r60S ribosomal subunit+40S ribosomal subunit+RRNA fragments+ mRNA fragments + tRNA – Cryo-EM
    • 3u5b, 3u5c, 3u5d, 3u5e, 3u5f, 3u5g, 3u5h, 3u5i, 4v88 - y60S ribosomal subunit+40S ribosomal subunit
    • 1vxu, 1vxv, 1vxw, 3j77, 3j78 - y60S ribosomal subunit+40S ribosomal subunit - rotated ribosome with 1 tRNA
    • 4u3m, 4u56, 4u3n, 4u55, 4u3u, 4u53, 4u4n, 4u4o, 4u4q, 4u4r, 4u4u, 4u52, 4u51, 4u4y, 4u4z, 4u6f, 4u50 - y60S ribosomal subunit+40S ribosomal subunit in complexes with 12 eukaryote-specific and 4 broad-spectrum inhibitors
  • 50S subunit + ribosome releasing factor (RRF)
    • 2rdo - Ec50S subunit+5S RRNA+23S RRNA+EF-G+RRF – Cryo-EM
    • 3j0d - Tt50S subunit+5S RRNA+23S RRNA+RRF – Cryo-EM
  • 50S subunit + various proteins
    • 2vhm - Ec50S subunit+5S RRNA+23S RRNA+PDF C-terminal helix
    • 2j28 - Ec50S subunit+5S RRNA+23S RRNA+signal recognition particle – Cryo-EM
    • 1vor, 1vou, 1vow, 1voy, 1vp0, 1pnu, 1pny - Ec50S subunit+5S RRNA+23S RRNA+general stress protein Ctc
    • 3j01 - Ec50S subunit+5S RRNA+23S RRNA + SECYE – Cryo-EM
    • 1w2b - Hm50S subunit+5S RRNA+23S RRNA+trigger factor N-terminal
  • 60S subunit + various proteins
    • 4a18, 4a19, 4a1b, 4a1d - Tet60S subunit+ 26S RRNA+ translation initiation factor 6
    • 3izs – y60S subunit + P0 + P1 + P2 - Cryo EM
    • 3u5i – y60S subunit + P0
    • 4b6a – y60S subunit + P0 + P1 + P2 + ARX1 - Cryo EM
    • 3o5h – y60S subunit + 5S RRNA + 5.8S RRNA + 25S RRNA + P0
    • 3j39 – Dm60S subunit + P0 - Cryo EM
    • 3j3b – h60S subunit + P0 + P1 + P2 – human - Cryo EM
    • 2lbf – hP1 dimerization domain + P2 dimerization domain - NMR
    • 2w1o – hP2 dimerization domain - NMR
    • 4beh – hP1 + P2 - NMR
  • Mitochondrial ribosome (mitoribosome)
    • 5aj4 - 28S small and 39S large subunit of the mammalian mitoribosome in a 55S complex - pig
    • 4v19 and 4v1a- 39S large subunit of the mammalian mitoribosome - pig
    • 5aj3 - 28S small subunit of the mammalian mitoribosome - pig
    • 4ce4 - 39S large subunit of the mammalian mitoribosome - pig
    • 3j6b - y54S large subunit of the mitoribosome
    • 3j6v - 28S small subunit of the mammalian mitoribosome - bovine
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