6XZ7: E. coli 50S ribosomal subunit
E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet). Determined by electron microscopy at 2.1 Å resolution. Released 22 Jul 2020.
- Method
- Electron microscopy
- Resolution
- 2.1 Å
- Organisms
- Escherichia coli (strain K12), Saccharomyces cerevisiae
- Chains
- 33
- Atoms
- 94,915
- Mol. weight
- 1404.32 kDa
- Ligands
- DI0, MG
- Released
- 22 Jul 2020
Explore 6XZ7 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6XZ7 contains 144 α-helices and 207 β-strands across 29 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 a: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| α-helix | 10-16 | 7 | |
| α-helix | 17-19 | 3 | |
| β-strand | 29-30 | 2 | 1 |
| β-strand | 37-38 | 2 | 1 |
| β-strand | 42 | 1 | 43 |
| β-strand | 48 | 1 | 2 |
| β-strand | 53 | 1 | 2 |
Chain b: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6 | 1 | |
| β-strand | 7-13 | 7 | 3 |
| β-strand | 20-25 | 6 | 3 |
| α-helix | 33-34 | 2 | |
| β-strand | 35-40 | 6 | 3 |
| β-strand | 45-53 | 9 | 3 |
Chain c: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-21 | 4 | |
| α-helix | 25-37 | 13 | |
Chain C: 7 helices, 30 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 4 |
| α-helix | 6-7 | 2 | |
| β-strand | 17-19 | 3 | 4 |
| β-strand | 24 | 1 | 5 |
| α-helix | 31-33 | 3 | |
| β-strand | 34-36 | 3 | 6 |
| β-strand | 43 | 1 | 7 |
| β-strand | 49 | 1 | 7 |
| β-strand | 54 | 1 | 8 |
| β-strand | 61-63 | 3 | 6 |
| β-strand | 65 | 1 | 5 |
| β-strand | 72 | 1 | 9 |
| β-strand | 76-82 | 7 | 5 |
| β-strand | 91-96 | 6 | 5 |
| β-strand | 101-105 | 5 | 5 |
| β-strand | 107 | 1 | 10 |
| β-strand | 115-116 | 2 | 5 |
| β-strand | 118 | 1 | 9 |
| β-strand | 129-131 | 3 | 9 |
| α-helix | 132-134 | 3 | |
| β-strand | 140-142 | 3 | 9 |
| β-strand | 144-145 | 2 | 11 |
| β-strand | 152-154 | 3 | 11 |
| β-strand | 162-168 | 7 | 9 |
| β-strand | 171-175 | 5 | 9 |
| β-strand | 181-185 | 5 | 9 |
| β-strand | 189-192 | 4 | 9 |
| β-strand | 195 | 1 | 10 |
| α-helix | 198-202 | 5 | |
| β-strand | 204 | 1 | 4 |
| α-helix | 208-213 | 6 | |
| β-strand | 216 | 1 | 8 |
| α-helix | 222-224 | 3 | |
| β-strand | 245 | 1 | 12 |
| β-strand | 251 | 1 | 12 |
| α-helix | 264-266 | 3 | |
| β-strand | 267-269 | 3 | 9 |
Chain d: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 8-11 | 4 | |
| β-strand | 15-16 | 2 | 16 |
| β-strand | 22-24 | 3 | 16 |
| α-helix | 38-43 | 6 | |
| β-strand | 48-49 | 2 | 16 |
| α-helix | 50-51 | 2 | |
| α-helix | 52-54 | 3 | |
| α-helix | 55-61 | 7 | |
Chain D: 9 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-16 | 13 | 13 |
| β-strand | 20-28 | 9 | 13 |
| α-helix | 31 | 1 | |
| β-strand | 32-38 | 7 | 14 |
| β-strand | 47-51 | 5 | 14 |
| α-helix | 57-59 | 3 | |
| α-helix | 62-71 | 10 | |
| β-strand | 79-83 | 5 | 14 |
| α-helix | 84-85 | 2 | |
| β-strand | 95-96 | 2 | 14 |
| α-helix | 98-101 | 4 | |
| β-strand | 106-112 | 7 | 13 |
| α-helix | 113-115 | 3 | |
| β-strand | 117-119 | 3 | 15 |
| α-helix | 121-125 | 5 | |
| α-helix | 127-129 | 3 | |
| α-helix | 155-156 | 2 | |
| β-strand | 163-165 | 3 | 15 |
| β-strand | 169-181 | 13 | 13 |
| β-strand | 186-190 | 5 | 13 |
| β-strand | 200-205 | 6 | 13 |
Chain e: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 19 |
| β-strand | 14-19 | 6 | 19 |
| β-strand | 22-27 | 6 | 19 |
| α-helix | 31-33 | 3 | |
| β-strand | 35-37 | 3 | 19 |
Chain E: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 17 |
| β-strand | 11-13 | 3 | 17 |
| α-helix | 16-19 | 4 | |
| α-helix | 25-39 | 15 | |
| α-helix | 93-95 | 3 | |
| α-helix | 98-114 | 17 | |
| β-strand | 118-121 | 4 | 18 |
| α-helix | 131-140 | 10 | |
| β-strand | 146-150 | 5 | 18 |
| α-helix | 155-162 | 8 | |
| β-strand | 167-171 | 5 | 18 |
| α-helix | 172-174 | 3 | |
| α-helix | 177-182 | 6 | |
| β-strand | 185-189 | 5 | 18 |
| α-helix | 190-199 | 10 | |
21 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 |
|---|
| 23S rRNA | A | RNA | 2897 | Escherichia coli (strain K12) | |
| 5S rRNA | B | RNA | 120 | Escherichia coli (strain K12) | |
| 50S ribosomal protein L2 | C | protein | 271 | Escherichia coli (strain K12) | P60422 (AlphaFold model) |
| 50S ribosomal protein L3 | D | protein | 209 | Escherichia coli (strain K12) | P60438 (AlphaFold model) |
| 50S ribosomal protein L4 | E | protein | 201 | Escherichia coli (strain K12) | P60723 (AlphaFold model) |
| 50S ribosomal protein L5 | F | protein | 177 | Escherichia coli (strain K12) | P62399 (AlphaFold model) |
| 50S ribosomal protein L6 | G | protein | 176 | Escherichia coli (strain K12) | P0AG55 |
| 50S ribosomal protein L10 | H | protein | 135 | Escherichia coli (strain K12) | P0A7J3 |
| 50S ribosomal protein L11 | I | protein | 134 | Escherichia coli (strain K12) | P0A7J7 |
| 50S ribosomal protein L13 | J | protein | 142 | Escherichia coli (strain K12) | P0AA10 |
| 50S ribosomal protein L14 | K | protein | 123 | Escherichia coli (strain K12) | P0ADY3 |
| 50S ribosomal protein L15 | L | protein | 144 | Escherichia coli (strain K12) | P02413 |
21 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6XZ7_1 23S rRNA (chains A)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCACUUACCAACCCGAU
GCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAACGUCCG
UCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGG
AAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAA
GAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACC
AUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUCUGUAAG
CCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAG
UAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUU
AAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAAC
AGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAUGUUGGC
CGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAU
CAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCA
GGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCA
GGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCC
GUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAGCUGAAA
UCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACAC
GAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUGGGGUUA
GCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACXAUAACGGUCCU
AAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCC
AGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCG
CGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUU
GAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCU
UGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUUGCGGAC
AGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACG
AAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGA
CUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGA
AUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCC
CAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGG
CUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCUGGGUUU
AGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAGGGGGGC
UGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAA
UGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAA
CUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGAAGACGA
CGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUACUAAUGA
ACCGUGAGGCUUAACCU
Sequence of entity 2 (B), FASTA
>6XZ7_2 5S rRNA (chains B)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU
Sequence of entity 3 (C), FASTA
>6XZ7_3 50S ribosomal protein L2 (chains C)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS
Sequence of entity 4 (D), FASTA
>6XZ7_4 50S ribosomal protein L3 (chains D)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 5 (E), FASTA
>6XZ7_5 50S ribosomal protein L4 (chains E)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 6 (F), FASTA
>6XZ7_6 50S ribosomal protein L5 (chains F)
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAIS
GQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKS
FDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR
Sequence of entity 7 (G), FASTA
>6XZ7_7 50S ribosomal protein L6 (chains G)
SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADG
WAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGI
TAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK
Sequence of entity 8 (H), FASTA
>6XZ7_8 50S ribosomal protein L10 (chains H)
ALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLLR
RAVEGTPFECLKDAFVGPTLIAYVTEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPAS
QIDRLATLPTYEEAI
Sequence of entity 9 (I), FASTA
>6XZ7_9 50S ribosomal protein L11 (chains I)
YVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSF
TFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTR
SIEGTARSMGLVVE
Sequence of entity 10 (J), FASTA
>6XZ7_10 50S ribosomal protein L13 (chains J)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI
Sequence of entity 11 (K), FASTA
>6XZ7_11 50S ribosomal protein L14 (chains K)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EVL
Sequence of entity 12 (L), FASTA
>6XZ7_12 50S ribosomal protein L15 (chains L)
MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRR
LPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPV
TVRGLRVTKGARAAIEAAGGKIEE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| DI0 | Dirithromycin | C42 H78 N2 O14 | 1 |
| MG | Magnesium ion | Mg | 178 |
Primary citation
Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to theE. coli70S ribosome. Pichkur, E.B., Paleskava, A., Tereshchenkov, A.G. et al. RNA (2020) 26:715-723. DOI 10.1261/rna.073817.119 · 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
Browse structure collections
About this viewer
MolViewer shows 6XZ7 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.