Ribosome 3D structures
From Proteopedia
Updated on 26-May-2014 For a general description of the protein see Ribosome
30S subunit + RNA
2zm6, 1n36, 1j5e, 3oto - Tt30S ribosomal subunit+THX+16S RRNA – Thermus thermophiles
2vqe, 2vqf, 2uuc, 2e5l, 2uu9, 2uua, 2uub, 3pyn, 3pyq, 3pys, 3pyu - Tt30S ribosomal subunit+16S RRNA+RNA fragment
3kc4 - Ec30S ribosomal subunit - Escherichia coli
3i1m, 3i1o, 3df1, 3df3, 2vho, 2vhp, 2avy, 2aw7, 1pnx - Ec30S ribosomal subunit+16S RRNA
1i94, 1fka, 3uxs, 3uxt, 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
1p87 - Ec30S ribosomal subunit+16S RRNA – Cryo-EM
3bbn - s30S ribosomal subunit+16S RRNA – Cryo-EM – spinach
30S subunit + chain release factor
3mr8, 3ms0 – Tt30S ribosomal subunit+THX+chain release factor 1+P-site tRNA+mRNA+16S RRNA
3d5a 3d5c - Tt30S ribosomal subunit+THX+chain release factor 1+P-site tRNA+E-site tRNA+mRNA +16S RRNA
3zvo - Tt30S ribosomal subunit+THX+P-site tRNA Met +mRNA +16S RRNA+chain release factor 3
2b64 - Tt30S ribosomal subunit+THX+P-site tRNA Phe+E-site tRNA Phe+mRNA +16S RRNA+chain release factor 1
2b9m - Tt30S ribosomal subunit+THX+P-site tRNA Phe+E-site tRNA Phe+mRNA +16S RRNA+chain release factor 2
2x9r, 2x9t, 2wh1, 2wh3 - Tt30S ribosomal subunit+THX+chain release factor 2+P-site tRNA+mRNA +16S RRNA
3f1e, 3f1g - Tt30S ribosomal subunit+THX+chain release factor 2+P-site tRNA+E-site tRNA +16S RRNA
4kfh, 4kfk - Tt30S ribosomal subunit+16S RRNA+ RF-2 + mRNA+ P-site tRNA fMet
30S subunit +tRNA+mRNA
2hgi - Tt30S ribosomal subunit+16S RRNA+tRNA Phe+tRNA fMet
4l6k, 4l6m - Tt30S ribosomal subunit+16S RRNA+tRNA Phe+tRNA
2hgp - Tt30S ribosomal subunit+16S RRNA+tRNA Phe+mRNA
3t1h, 3t1y - Tt30S ribosomal subunit+16S RRNA+tRNA Lys +mRNA
3tvf, 3tvg, 3uyd, 3uyf - Tt30S ribosomal subunit+16S RRNA+tRNA Leu + tRNA fMet + mRNA
3zn7, 3znd - Tt30S ribosomal subunit+16S RRNA+A-site tRNA Ile agmatidine + E-site tRNA Ile agmatidine + mRNA
3uz6, 3uz7, 3uzg, 3uzi - Tt30S ribosomal subunit+16S RRNA+tRNA Tyr + tRNA fMet + mRNA
2i2p, 2i2u - Ec30S ribosomal subunit+16S RRNA+tRNA Phe+mRNA
2hgr, 3v6u, 3v6v, 4ej9, 4eja - Tt30S ribosomal subunit+16S RRNA+tRNA Phe+tRNA fMet+mRNA
1yl4 – Tt30S ribosomal subunit+ tRNA Phe+16S RRNA+THRS mRNA operator
1pns - Ec30S ribosomal subunit+ tRNA Phe+16S RRNA+mRNA
3j13 - Ec30S ribosomal subunit+ P-site tRNA +16S RRNA+mRNA – Cryo-EM
3j0u, 3j0v, 3j0x, 3j0z, 3j10, 3j20 - Ec30S ribosomal subunit+ A-site tRNA + P-site tRNA +16S RRNA+mRNA – Cryo-EM
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, 4k0l - 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
3i8g - Tt30S ribosomal subunit+P-site tRNA+mRNA +16S RRNA
3i8h, 3i9b, 3i9d - Tt30S ribosomal subunit+THX+P-site tRNA+mRNA +16S RRNA
1ibk - Tt30S ribosomal subunit+THX+P-site mRNA fragment +16S RRNA
2wwl - Ec30S ribosomal subunit+Poly-Ala chain+P-site tRNA+mRNA +16S RRNA
3i1q - Ec30S ribosomal subunit+P-site tRNA hairpin+mRNA
3i1s, 3i1z, 3i21 - Ec30S ribosomal subunit+P-site tRNA hairpin+mRNA +16S RNA
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+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
4k0p - Tt30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA +mRNA +16S RRNA
3e1a, 3e1c - Ec30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+mRNA +16S RRNA
30S subunit + antibiotics
1i95, 1i97, 2hhh, 2f4v, 3oge, 3ogy, 3ohc, 3ohd, 3ohy, 3oi0, 3oi2, 3oi4, 4dr3 - Tt30S ribosomal subunit+16S RRNA+antibiotic
1hnx, 1hnw, 1hnz, 1fjg, 4aqy, 4dr5, 4dr6, 4dr7, 4khp - Tt30S ribosomal subunit+16S RRNA+mRNA fragment+antibiotic
2qbb, 2qb9, 1vs5, 1vs7 , 2qan, 2qal, 2qou, 2qow, 2qoy, 2qp0, 2z4k, 2z4m, 3oaq, 3oar, 3ofa, 3ofb, 3ofo, 3ofp, 3ofx, 3ofy, 3or9, 3ora - Ec30S ribosomal subunit+16S RRNA+antibiotic
4gaq, 4gas - Ec30S ribosomal subunit+16S RRNA+ mRNA + antibiotic
3sfs - Ec30S ribosomal subunit+16S RRNA+ mRNA + RF-3 + antibiotic
2j00, 2j02 - Tt30S ribosomal subunit+16S RRNA+paromomycin+P-site tRNA fMet+E-site tRNA Phe+mRNA
3knl, 3knm, 3knn, 3kno, 3knj, 3knh - Tt30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+mRNA +16S RRNA+ antibiotic
3uz3, 3uz4 - Tt30S ribosomal subunit+16S RRNA+tRNA Leu + tRNA fMet + mRNA + paromomycin
4g5k, 4g5m, 4g5t, 4g5v - Tt30S ribosomal subunit+16S RRNA + tRNA fMet + mRNA + antibiotics
3uzl, 3uzm - Tt30S ribosomal subunit+16S RRNA+tRNA Tyr + tRNA fMet + mRNA + paromomycin
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
2x9s, 2x9u, 3kni, 3knk, 3knm, 3kno, 3hux, 3huz, 2wdi, 2wdj 2wdl 1vsp, 2v47 , 2v49, 1vsa, 3pyo, 3pyr, 3pyt, 3pyv, 3v6w, 3v6x, 3zne, 4btd, 4ejb, 4ejc, 4k0m, 4k0q, 2wrj, 2wrl, 2wro, 2wrr, 2wh2, 2wh4, 2hgj, 2hgq, 2hgu,2j01, 2j03, 1yl3, 3i8i, 3f1f, 3f1h, 2b66, 2b9n, 2b9p, 1giy, 2xqe, 2y0v, 2y0x, 2y0z, 2y11, 2y13, 2y15, 2y17, 2y19, 3zvp, 4abs, 4b8g, 4b8i, 4jux, 4kbu, 4kbw, 4kcz, 4kd2, 4kd9, 4kdb, 4kdh, 4kdk, 4kfi, 4kfl - Tt50S subunit+5S RRNA+23S RRNA
2xg0, 2xg2, 3kir, 3kit, 3kiw, 3kiy – Tt50S subunit+RNA fragments
3fin, 2xtg, 2xux - Tt50S subunit+5S RRNA+23S RRNA – Cryo-EM
2wwq – Ec 50S subunit+5S RRNA+23S RRNA+mRNA+P-site tRNA
3i1n, 3i1p, 3i1r, 3i1t, 3i20, 3i22, 3e1b, 3e1d, 3df2, 3df4, 2vhn, 2qov, 2qox, 2i2t, 2i2v, 1vs6, 1vs8, 2aw4, 2awb, 3ofd, 3og0, 3oas, 3oat, 3uos, 3r8s, 3r8t, 3j37, 4kix, 4kiz, 4kj1, 4kj3, 4kj5, 4kj7, 4kj9, 4kjb - Ec50S subunit+5S RRNA+23S RRNA
3fik, 2gya, 2gyc, 1p85, 1p86, 3izt, 3izu, 3j0t, 3j0w, 3j0y, 3j11, 3j12, 3j14, 3j19 - Ec50S subunit+5S RRNA+23S RRNA – Cryo-EM
3kcr - Ec50S subunit+5S RRNA+23S RRNA+preprotein translocase
3bbo - s50S subunit+5S RRNA+23S RRNA+4.8S RRNA – Cryo-EM
2zjq, 2zjr, 1nkw - Dr50S subunit+5S RRNA+23S RRNA – Deinococcus radiodurans
2qa4, 3cc2, 1s72, 4hub, 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
3j21 – 50S subunit + P0 + LX – Pyrococcus furiosus – 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
2qba, 2qbc, 4gar, 4gau, 2qam, 2qao, 2qoz, 2qp1, 3ofc, 3ofz, 3ofq, 3ofr, 1vt2, 3orb, 4l6j, 4l6l - Ec50S 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
3oh5, 3oh7, 3ohj, 3ohk, 3ohz, 3oi1, 3oi3, 3oi5 - Tt50S subunit+5S RRNA+23S RRNA+antibiotic
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
2zkr - d60S ribosomal subunit+30S ribosomal subunit+28S RRNA+5.8S RRNA – Cryo-EM
3j0l - r60S ribosomal subunit+40S ribosomal subunit+RRNA fragments+ mRNA fragments – Cryo-EM
3j0o, 3j0p, 3j0q - r60S ribosomal subunit+40S ribosomal subunit+RRNA fragments+ mRNA fragments + tRNA – Cryo-EM
50S subunit + ribosome releasing factor (RRF)
2qbe, 2qbg, 2qbi, 2qbk, 2z4l, 2z4n - Ec50S subunit+5S RRNA+23S RRNA+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 - Ec 50S 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 – Drosophila melanogaster - Cryo EM
3j3b – h60S subunit + P0 + P1 + P2 – human - Cryo EM
Proteopedia Page Contributors and Editors (what is this?)
Michal Harel, Wayne Decatur, Joel L. Sussman, Jaime Prilusky, Alexander Berchansky
