5UYM: 70S ribosome
70S ribosome bound with cognate ternary complex base-paired to A site codon, closed 30S (Structure III). Determined by electron microscopy at 3.2 Å resolution. Released 7 Jun 2017.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organism
- Escherichia coli (strain K12)
- Chains
- 60
- Atoms
- 154,139
- Mol. weight
- 2297.89 kDa
- Ligands
- GCP, PHE, FME, ZN
- Released
- 7 Jun 2017
Explore 5UYM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5UYM contains 256 α-helices and 371 β-strands across 53 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain 03: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-14 | 9 | |
| α-helix | 20 | 1 | |
| β-strand | 21 | 1 | 119 |
| α-helix | 22 | 1 | |
| α-helix | 23-29 | 7 | |
| β-strand | 41-47 | 7 | 120 |
| α-helix | 55-57 | 3 | |
| β-strand | 60-63 | 4 | 121 |
| β-strand | 161-164 | 4 | 121 |
| β-strand | 170-177 | 8 | 120 |
| α-helix | 182-197 | 16 | |
| β-strand | 212-215 | 4 | 120 |
| β-strand | 222-223 | 2 | 120 |
| β-strand | 224 | 1 | 119 |
Chain 04: 5 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 1 |
| α-helix | 5-6 | 2 | |
| β-strand | 16-18 | 3 | 1 |
| α-helix | 30-32 | 3 | |
| β-strand | 33-34 | 2 | 2 |
| β-strand | 42 | 1 | 3 |
| β-strand | 48 | 1 | 3 |
| β-strand | 53 | 1 | 4 |
| β-strand | 61-62 | 2 | 2 |
| β-strand | 64 | 1 | 5 |
| β-strand | 75-80 | 6 | 5 |
| β-strand | 90-95 | 6 | 5 |
| β-strand | 100-104 | 5 | 5 |
| α-helix | 105 | 1 | |
| β-strand | 106 | 1 | 6 |
| β-strand | 114-115 | 2 | 5 |
| β-strand | 117 | 1 | 7 |
| β-strand | 128-130 | 3 | 7 |
| β-strand | 139-141 | 3 | 7 |
| β-strand | 143 | 1 | 8 |
| β-strand | 153 | 1 | 8 |
| β-strand | 161-167 | 7 | 7 |
| β-strand | 170-174 | 5 | 7 |
| β-strand | 180-184 | 5 | 7 |
| β-strand | 188-191 | 4 | 7 |
| β-strand | 194 | 1 | 6 |
| α-helix | 199-201 | 3 | |
| β-strand | 203 | 1 | 1 |
| α-helix | 208-211 | 4 | |
| β-strand | 215 | 1 | 4 |
| β-strand | 244 | 1 | 9 |
| β-strand | 250 | 1 | 9 |
| β-strand | 266-268 | 3 | 7 |
Chain 05: 3 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-11 | 8 | 12 |
| β-strand | 14-15 | 2 | 13 |
| β-strand | 21-22 | 2 | 13 |
| β-strand | 24-28 | 5 | 12 |
| β-strand | 32-38 | 7 | 14 |
| β-strand | 47-52 | 6 | 14 |
| α-helix | 62-71 | 10 | |
| β-strand | 77-83 | 7 | 14 |
| β-strand | 95-96 | 2 | 14 |
| α-helix | 98-101 | 4 | |
| β-strand | 106-112 | 7 | 12 |
| β-strand | 115-119 | 5 | 15 |
| α-helix | 121-124 | 4 | |
| β-strand | 163-166 | 4 | 15 |
| β-strand | 169-179 | 11 | 12 |
| β-strand | 188-190 | 3 | 12 |
| β-strand | 200-205 | 6 | 12 |
Chain 06: 10 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 18 |
| β-strand | 12-13 | 2 | 18 |
| α-helix | 16-19 | 4 | |
| α-helix | 25-39 | 15 | |
| α-helix | 68-69 | 2 | |
| α-helix | 86-88 | 3 | |
| α-helix | 98-114 | 17 | |
| β-strand | 118-121 | 4 | 19 |
| α-helix | 131-138 | 8 | |
| β-strand | 146-150 | 5 | 19 |
| α-helix | 155-160 | 6 | |
| β-strand | 167-171 | 5 | 19 |
| α-helix | 172-174 | 3 | |
| α-helix | 177-182 | 6 | |
| β-strand | 185-189 | 5 | 19 |
| α-helix | 190-200 | 11 | |
Chain 07: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| α-helix | 7-11 | 5 | |
| α-helix | 12-16 | 5 | |
| β-strand | 30-37 | 8 | 20 |
| α-helix | 41-43 | 3 | |
| α-helix | 46-59 | 14 | |
| β-strand | 65-68 | 4 | 20 |
| α-helix | 69 | 1 | |
| β-strand | 83-90 | 8 | 20 |
| α-helix | 94-101 | 8 | |
| α-helix | 102-106 | 5 | |
| β-strand | 121 | 1 | 20 |
| β-strand | 127-130 | 4 | 20 |
| β-strand | 152-157 | 6 | 20 |
| α-helix | 162-170 | 9 | |
Chain 08: 6 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8 | 1 | 22 |
| β-strand | 15-19 | 5 | 23 |
| β-strand | 22-26 | 5 | 23 |
| β-strand | 31-35 | 5 | 23 |
| α-helix | 36-37 | 2 | |
| β-strand | 40-43 | 4 | 24 |
| β-strand | 49 | 1 | 22 |
| β-strand | 50-53 | 4 | 24 |
| α-helix | 54 | 1 | |
| α-helix | 60-79 | 20 | |
| β-strand | 82-89 | 8 | 25 |
| β-strand | 94-97 | 4 | 26 |
| β-strand | 101-105 | 5 | 26 |
| β-strand | 112-115 | 4 | 26 |
| α-helix | 116 | 1 | |
| β-strand | 120-123 | 4 | 25 |
| β-strand | 129-134 | 6 | 25 |
| α-helix | 137-150 | 14 | |
| α-helix | 152-154 | 3 | |
| β-strand | 160-163 | 4 | 25 |
Chain 09: 9 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-5 | 2 | 28 |
| β-strand | 18 | 1 | 28 |
| α-helix | 23-25 | 3 | |
| α-helix | 26-30 | 5 | |
| α-helix | 31-33 | 3 | |
| β-strand | 36-37 | 2 | 28 |
| α-helix | 41-45 | 5 | |
| α-helix | 46-55 | 10 | |
| α-helix | 56-62 | 7 | |
| α-helix | 65-69 | 5 | |
| β-strand | 77-80 | 4 | 29 |
| β-strand | 84 | 1 | 30 |
| β-strand | 90 | 1 | 30 |
| α-helix | 96-104 | 9 | |
| α-helix | 112-114 | 3 | |
| β-strand | 126-130 | 5 | 29 |
| β-strand | 142-146 | 5 | 29 |
Chain 10: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-18 | 15 | |
| β-strand | 24 | 1 | 34 |
| α-helix | 41-47 | 7 | |
| α-helix | 64-66 | 3 | |
| α-helix | 72-76 | 5 | |
| α-helix | 97-103 | 7 | |
| α-helix | 111-113 | 3 | |
| β-strand | 117 | 1 | 34 |
45 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 50S ribosomal protein L2 | 04 | protein | 271 | Escherichia coli (strain K12) | P60422 (AlphaFold model) |
| 50S ribosomal protein L3 | 05 | protein | 209 | Escherichia coli (strain K12) | P60438 (AlphaFold model) |
| 50S ribosomal protein L4 | 06 | protein | 201 | Escherichia coli (strain K12) | P60723 (AlphaFold model) |
| 50S ribosomal protein L5 | 07 | protein | 177 | Escherichia coli (strain K12) | P62399 (AlphaFold model) |
| 50S ribosomal protein L6 | 08 | protein | 176 | Escherichia coli (strain K12) | P0AG55 |
| 50S ribosomal protein L9 | 09 | protein | 149 | Escherichia coli (strain K12) | P0A7R1 |
| 50S ribosomal protein L10 | 10 | protein | 131 | Escherichia coli (strain K12) | P0A7J3 |
| 50S ribosomal protein L11 | 11 | protein | 141 | Escherichia coli (strain K12) | P0A7J7 |
| 50S ribosomal protein L13 | 12 | protein | 142 | Escherichia coli (strain K12) | P0AA10 |
| 50S ribosomal protein L14 | 13 | protein | 122 | Escherichia coli (strain K12) | P0ADY3 |
| 50S ribosomal protein L15 | 14 | protein | 143 | Escherichia coli (strain K12) | P02413 |
| 50S ribosomal protein L16 | 15 | protein | 136 | Escherichia coli (strain K12) | P0ADY7 |
47 more molecules are not listed.
Sequence of entity 1 (04), FASTA
>5UYM_1 50S ribosomal protein L2 (chains 04)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS
Sequence of entity 2 (05), FASTA
>5UYM_2 50S ribosomal protein L3 (chains 05)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 3 (06), FASTA
>5UYM_3 50S ribosomal protein L4 (chains 06)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 4 (07), FASTA
>5UYM_4 50S ribosomal protein L5 (chains 07)
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAIS
GQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKS
FDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR
Sequence of entity 5 (08), FASTA
>5UYM_5 50S ribosomal protein L6 (chains 08)
SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADG
WAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGI
TAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK
Sequence of entity 6 (09), FASTA
>5UYM_6 50S ribosomal protein L9 (chains 09)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE
Sequence of entity 7 (10), FASTA
>5UYM_7 50S ribosomal protein L10 (chains 10)
MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLL
RRAVEGTPFECLKDAFVGPTLIAYSMEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPA
SQIDRLATLPT
Sequence of entity 8 (11), FASTA
>5UYM_8 50S ribosomal protein L11 (chains 11)
AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITV
YADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGAD
IEAMTRSIEGTARSMGLVVED
Sequence of entity 9 (12), FASTA
>5UYM_9 50S ribosomal protein L13 (chains 12)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI
Sequence of entity 10 (13), FASTA
>5UYM_10 50S ribosomal protein L14 (chains 13)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EV
Sequence of entity 11 (14), FASTA
>5UYM_11 50S ribosomal protein L15 (chains 14)
RLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRL
PKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVT
VRGLRVTKGARAAIEAAGGKIEE
Sequence of entity 12 (15), FASTA
>5UYM_12 50S ribosomal protein L16 (chains 15)
MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQ
GKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLA
AAKLPIKTTFVTKTVM
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GCP | Phosphomethylphosphonic acid guanylate ester | C11 H18 N5 O13 P3 | 1 |
| PHE | Phenylalanine | C9 H11 N O2 | 1 |
| FME | N-formylmethionine | C6 H11 N O3 S | 1 |
| ZN | Zinc ion | Zn | 2 |
| MG | Magnesium ion | Mg | 383 |
Primary citation
Ensemble cryo-EM elucidates the mechanism of translation fidelity. Loveland, A.B., Demo, G., Grigorieff, N. et al. Nature (2017) 546:113-117. DOI 10.1038/nature22397 · PubMed
Other PDB entries of the same protein (UniProt P60422 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8B0X 1.55 Å, Translating 70S ribosome in the unrotated state (P and E, tRNAs)
- 9Q87 1.55 Å, Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom…
- 8CGK 1.64 Å, Lincomycin and Avilamycin bound to the 50S subunit
- 8CGV 1.66 Å, Tiamulin bound to the 50S subunit
- 8CEU 1.83 Å, Retapamulin and Capreomycin bound to the 50S subunit
- 8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
- 8CAM 1.86 Å, Evernimicin bound to the 50S subunit
- 9GHE 1.87 Å, Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S…
- 9T0Y 1.87 Å, E. coli 70S ribosome from delta-9 strain
- 9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
- 9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
- 8E30 1.91 Å, E. coli 50S ribosome bound to compound streptogramin A analog 3142
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