Ribosome 3D structures

From Proteopedia

Revision as of 08:04, 24 November 2016

Updated on 24-November-2016 For a general description of the protein see Ribosome {{#tree:id=OrganizedByTopic|openlevels=0|

• 30S subunit + RNA

• • 2zm6, 1n36, 1j5e, 3oto - Tt30S ribosomal subunit+THX+16S RRNA – Thermus thermophiles
    
  • 2vqe, 2vqf, 2uuc, 2e5l]], 2uu9, 2uua, 2uub - Tt30S ribosomal subunit+16S RRNA+RNA fragment
    
  • 3i1m, 3i1o

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

• • 4duy, 4duz, 4dv0, 4dv1, 4dv2, 4dv3, 4dv4, 4dv5, 4dv6, 4dv7 - Tt30S ribosomal subunit+16S RRNA (mutant)
    
  • 4dr4, 4b3m, 4b3r, 4b3s, 4b3t - Tt30S ribosomal subunit+16S RRNA + mRNA
    

• 30S subunit +tRNA+mRNA

• • 3t1h, 3t1y - Tt30S ribosomal subunit+16S RRNA+tRNA Lys +mRNA
    
  • 3v6u, 3v6v - Tt30S ribosomal subunit+16S RRNA+tRNA Phe+tRNA fMet+mRNA
    

omal subunit+ tRNA Phe+16S RRNA+THRS mRNA operator

• • 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
    

• 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

• • 1i95, 1i97, 2hhh, 2f4v, 4dr3 - Tt30S ribosomal subunit+16S RRNA+antibiotic
    
  • 1hnx, 1hnw, 1hnz, 1fjg, 4aqy, 4dr5, 4dr6, 4dr7, 4khp - Tt30S ribosomal subunit+16S RRNA+mRNA fragment+antibiotic
    
  • 3knj, 3knh - Tt30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+mRNA +16S RRNA+ antibiotic
    

• 30S subunit + ribosome recycling factor

• • 3r8n, 3r8o - Ec30S ribosomal subunit+16S RRNA+ribosome recycling factor + mRNA + tRNA - Escherichia coli
    

• 30S subunit + elongation factor

• • 4btc - Tt30S ribosomal subunit+THX+RNA +16S RRNA+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

• • 1x18 – TtRPS2+TtRPS7+TtRPS11+TtRPS18+GTP-binding protein ERA+RNA fragments
    
  • 2ykr - EcRPS2 + 16S RRNA + GMPPNP + GTPase RSGA
    
  • 4a2i - EcRPS2 + 16S RRNA + GTPase RSGA – Cryo EM
    
  • 4adv - EcRPS2 + 16S RRNA + methyltransferase – Cryo EM
    

• 40S ribosomal subunit

• • 4v5o - Tet40S ribosomal subunit+RACK1 – Tetrahymena thermophila
    
  • 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
    
  • 4bts - r40S ribosomal subunit+ 18SRRNA + EIF1 + EIF1A
    

*50S subunit+RNA

• • 3kni, 3knk, 3knm, 3kno, 3v6w, 3v6x, 3zne, 4k0m, 4k0q, - Tt50S subunit+5S RRNA+23S RRNA
    
  • 3i1n, 3i1p, - Ec50S subunit+5S RRNA+23S RRNA
    
  • 2zjq, 2zjr, 1nkw - Dr50S subunit+5S RRNA+23S RRNA – Deinococcus radiodurans
    
  • 2qa4, 3cc2, 1s72, 4v9f, 1kqs, 1qvg, 1jj2, 1ffk - Hm50S subunit+5S RRNA+23S RRNA – Haloarcula marismortui
    
  • 3cc7, 3cce, 3ccj, 3ccl, 3ccm, 3ccq, 3ccr, 3ccs, 3ccu, 3ccv - Hm50S subunit+5S RRNA+23S RRNA (mutant)
    
  • 1yj9 - Hm50S subunit (mutant)+5S RRNA+23S RRNA
    
  • 1qvf- Hm50S subunit+5S RRNA+23S RRNA + deacylated tRNA minihelix
    
  • [1q86]] - Hm50S subunit+5S RRNA+23S RRNA+CCA-Phe-caproic acid-biotin
    
  • 3cma, 3cme, 1vq8, 1vq9, 1m90 - Hm50S subunit+5S RRNA+23S RRNA+CCA+CCA-Phe-CAP-BIO
    
  • 1vq4, 1vq5, 1vq7, 1vql, 1vqm, 1vqp – Hm50S subunit+5S RRNA+23S RRNA+transition state analog
    
  • 1vq6, 1vqk, 1vqn – Hm50S subunit+5S RRNA+23S RRNA+ c-hpmn+CCA-Phe-caproic acid-biotin
    
  • 1vqo – Hm50S subunit+5S RRNA+23S RRNA+ CCPMN
    
  • 3iy9 – 50S subunit – Leishmania taretolae
    
  • 2ftc – 50S subunit+5S RRNA+23S RRNA – bovine - Cryo_EM
    
  • 3j3v, 3j3w - 50S subunit+5S RRNA+23S RRNA – Bacillus subtilis
    

*50S subunit + antibiotics

• • 3dll, 2zjp, 3cf5, 1xbp, 1sm1, 1nwx, 1nwy, 3pio, 3pip - Dr50S subunit+5S RRNA+23S RRNA+general stress protein Ctc+ antibiotic
    
  • 4io9, 4ioa, 4ioc - Dr50S subunit+5S RRNA+23S RRNA+ antibiotics
    
  • 3i55, 3i56 , 3g4s, 3g4e, 3g71, 2qex, 3cc4, 3cd6, 1yhq, 1yi2, 1yij, 1yjn, 1yjw, 2otj, 2otl, 1yit, 1k73, 1kc8, 1k8a, 1k9m, 1kd1, 1m1k, 3cpw, 1yit, 1q7y, 1q81, 1q82, 1n8r, 1nji, 3cxc - Hm50S subunit+5S RRNA+23S RRNA + antibiotics
    

*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

• • 2j28 - Ec50S subunit+5S RRNA+23S RRNA+signal recognition particle – Cryo-EM
    
  • 1w2b - Hm50S subunit+5S RRNA+23S RRNA+trigger factor N-terminal
    

• 60S subunit + various proteins

• • 4v8p - Tet60S subunit+ 26S RRNA+ translation initiation factor 6
    
  • 3izs – y60S subunit + P0 + P1 + P2 – yeast - Cryo EM
    
  • 4v8t – y60S subunit + P0 + P1 + P2 + ARX1 - Cryo EM
    
  • 3o5h – y60S subunit + 5S RRNA + 5.8S RRNA + 25S RRNA + P0
    
  • 3j39 – Dm60S subunit + P0 – Drosophila melanogaster - 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
    

• 70S ribosome

• • 4v4q, 4v9d - EcRibosome
    
  • 4v4i, 4v83, 4v84, 4v4s, 4v4x, 4v4z, 4v90, 4v42 – TtRibosome
    
  • 4v8j, 4v97 – TtRibosome ram mutation
    
  • 4v8n – TtRibosome agmatidine mutation
    
  • 4v6c, 4v6d, 4v6e – EcRibosome ratcheting
    
  • 4v69, 4v48, 4v4a – EcRibosome – Cryo-EM
    
  • 4v6u – Ribosome – Pyrococcus furiosus - Cryo-EM
    
  • 4v4y, 4v4j – TtRibosome Shine-Dalgarno duplex
    
  • 4v4v – EcRibosome pre-translocational – Cryo-EM
    
  • 4v5m – TtRibosome pre-translocational – Cryo-EM
    
  • 4v5n – TtRibosome post-translocational – Cryo-EM
    
  • 4v4w – EcRibosome SecM-stalled – Cryo-EM
    
  • 4v65 – EcRibosome pre-accomodation – Cryo-EM
    
  • 4v66 – EcRibosome post-accomodation – Cryo-EM
    
  • 4v61 – sRibosome – spinach - Cryo-EM
    
  • 4v8m - TbRibosome – Trypanosoma brucei – Cryo-EM
    

• 70S ribosome complex with mRNA

• • 4v50 – EcRibosome + mRNA
    
  • 4v6n, 4v6o, 4v6p, 4v6q, 4v6r, 4v6s – EcRibosome + mRNA – Cryo-EM
    
  • 4v6f, 4v6g , 4v87, 4v8b , 4v8d, 4v8e, 4v9i – TtRibosome + mRNA
    
  • 4v4t – TtRibosome + stop codon
    
  • 4v4p – TtRibosome + THRS mRNA operator
    

• 70S ribosome complex with antibiotic

• • 4v52, 4v53, 4v56, 4v57, 4v64, 4v4h, 4v7s, 4v7t, 4v7u, 4v7v, 4www – EcRibosome + antibiotic
    
  • 4v54 – EcRibosome + RRF
    
  • 4v55, 4v5y – EcRibosome + antibiotic + RRF
    
  • 4v51, 4v5c, 4v5d, 4v7w, 4v7x, 4v7y, 4v7z, 4v8a, 4v9c – TtRibosome + antibiotic
    
  • 4v8c, 4v8f, 4v9a, 4v9b, 4v9c – TtRibosome + mRNA + antibiotic
    
  • 4v7l, 4v7m – Ribosome + antibiotic – Streptomyces puniceus
    

• 70S ribosome complex with release factor

• • 4v5a – TtRibosome + RRF
    
  • 4v63, 4v7p – TtRibosome + RF-1
    
  • 4v5e, 4v4r, 4v67, 4v9n – TtRibosome + RF-2
    
  • 4v5j – TtRibosome + RF-2 + substrate analog
    
  • 1ml5 – EcRibosome + RF-2 – Cryo-EM
    
  • 4v89 – EcRibosome + RF-3
    
  • 4v85 – EcRibosome + RF-3 + mRNA + antibiotic
    
  • 4v8o – TtRibosome + RF-3
    

• 70S ribosome complex with various proteins

• • 4v5b – EcRibosome + PDF-binding helix
    
  • 4v5h – EcRibosome + Tnac leader peptide
    
  • 4v5k – TtRibosome + colicin E3
    
  • 4v6v - EcRibosome+ tetracycline resistance protein + mRNA + P-tRNA – Cryo-EM
    
  • 4v7j, 4v7k – TtRibosome + toxin RelE
    
  • 4v6m – EcRibosome + SecYE – Cryo-EM
    
  • 4v4g – EcRibosome + protein Y – 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
    

• 70S ribosome complex with elongation factor

• • 4v5f, 4v8u, 4v9h – TtRibosome + elongation factor G
    
  • 4v9o – EcRibosome + elongation factor G
    
  • 4v9p – EcRibosome + antibiotic + elongation factor G
    
  • 4v47 – EcRibosome + elongation factor G – Cryo-EM
    
  • 4v6t – EcRibosome + elongation factor G + tRNA-SmpB – Cryo-EM
    
  • [[4v56a] – TtRibosome + elongation factor P
    
  • 4v6k, 4v6l – EcRibosome + elongation factor Tu
    
  • 4v5l – EcRibosome + elongation factor Tu + tRNA
    
  • 4v5g – TtRibosome + elongation factor Tu
    
  • 4v8q – TtRibosome + antibiotic + elongation factor Tu
    
  • 4v68 – TtRibosome + antibiotic + elongation factor Tu – Cryo-EM
    
  • 4v5p, 4v5q, 4v5r, 4v5s – TtRibosome + elongation factor Tu + tRNA-Trp
    
  • 4v9j, 4v9k, 4v9l, 4v9m – TtRibosome + elongation factor G + tRNA
    
  • 4v9l – TtRibosome + elongation factor G + antibiotic + tRNA
    

• 80S ribosome

• • 4v6w - DmRibosome + elongation factor 2 + guanine nucleotide-binding protein – Drosophila melanogaster – Cryo-EM
    
  • 4v7r, 4v88 – yRibosome
    
  • 4v6i – yRibosome - Cryo-EM
    
  • 4v4b – yRibosome + elongation factor 2 + antifungal - Cryo-EM
    
  • 4v7e – Ribosome – wheat - Cryo-EM
    
  • 4v6x – Ribosome – human - Cryo-EM
    
  • 4v5z - dRibosome – Cryo-EM
    
  • 3j0l, 3j0o, 3j0p, 3j0q - rRibosome+ mRNA – Cryo-EM
    
  • 4v7h - TlRibosome+P-site tRNA – Thermomyces lanuginosus
    

• 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
    

}}