7QQ3: E.coli 50S ribosomal subunit
Cryo-EM structure of the E.coli 50S ribosomal subunit in complex with the antibiotic Myxovalargin A. Determined by electron microscopy at 2.1 Å resolution. Released 18 Jan 2023.
- Method
- Electron microscopy
- Resolution
- 2.1 Å
- Organisms
- Escherichia coli K-12, Myxococcus fulvus
- Chains
- 29
- Atoms
- 87,594
- Mol. weight
- 1311.84 kDa
- Ligands
- ZN, MG
- Released
- 18 Jan 2023
Explore 7QQ3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7QQ3 contains 119 α-helices and 183 β-strands across 27 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: 6 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-10 | 9 | 40 |
| α-helix | 14-24 | 11 | |
| β-strand | 28 | 1 | 40 |
| α-helix | 29-37 | 9 | |
| α-helix | 42-61 | 20 | |
| α-helix | 66-68 | 3 | |
| β-strand | 70-78 | 9 | 40 |
| α-helix | 80-81 | 2 | |
| β-strand | 82-87 | 6 | 41 |
| α-helix | 89-91 | 3 | |
| β-strand | 93-98 | 6 | 41 |
| β-strand | 101-108 | 8 | 40 |
Chain b: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-10 | 7 | |
| β-strand | 11-14 | 4 | 42 |
| α-helix | 19-27 | 9 | |
| β-strand | 29-34 | 6 | 42 |
| α-helix | 40-50 | 11 | |
| β-strand | 55-63 | 9 | 42 |
| α-helix | 64-66 | 3 | |
| β-strand | 67-70 | 4 | 43 |
| β-strand | 73-76 | 4 | 43 |
| α-helix | 77-79 | 3 | |
| β-strand | 80-87 | 8 | 42 |
Chain B: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-10 | 3 | |
Chain c: 2 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-13 | 4 | 44 |
| β-strand | 22-24 | 3 | 44 |
| β-strand | 25-29 | 5 | 45 |
| β-strand | 33-36 | 4 | 45 |
| β-strand | 41-45 | 5 | 46 |
| α-helix | 46-48 | 3 | |
| β-strand | 58-62 | 5 | 46 |
| β-strand | 65-66 | 2 | 45 |
| α-helix | 67-69 | 3 | |
| β-strand | 70-73 | 4 | 44 |
| β-strand | 80-81 | 2 | 44 |
| β-strand | 83-88 | 6 | 47 |
| β-strand | 91-96 | 6 | 47 |
| β-strand | 102 | 1 | 47 |
Chain d: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-8 | 6 | 48 |
| α-helix | 14-22 | 9 | |
| β-strand | 25-31 | 7 | 48 |
| α-helix | 36-37 | 2 | |
| β-strand | 38-43 | 6 | 48 |
| α-helix | 44-51 | 8 | |
| α-helix | 54-57 | 4 | |
| β-strand | 61-65 | 5 | 48 |
| β-strand | 68-79 | 12 | 48 |
| α-helix | 80 | 1 | |
| β-strand | 86-93 | 8 | 48 |
Chain e: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| β-strand | 22-23 | 2 | 49 |
| β-strand | 30-31 | 2 | 50 |
| β-strand | 36-39 | 4 | 49 |
| β-strand | 45-47 | 3 | 50 |
| β-strand | 51-53 | 3 | 49 |
| β-strand | 59-61 | 3 | 49 |
| β-strand | 65-72 | 8 | 50 |
| β-strand | 77-83 | 7 | 50 |
Chain f: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-18 | 6 | 51 |
| β-strand | 24-29 | 6 | 51 |
| β-strand | 33-40 | 8 | 52 |
| β-strand | 45-52 | 8 | 52 |
| α-helix | 53-62 | 10 | |
| α-helix | 64-74 | 11 | |
Chain g: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| α-helix | 11-34 | 24 | |
| α-helix | 41-61 | 21 | |
19 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 ribosomal RNA | I | RNA | 2904 | Escherichia coli K-12 | |
| 5S ribosomal RNA | J | RNA | 120 | Escherichia coli K-12 | |
| 50S ribosomal protein L2 | K | protein | 273 | Escherichia coli K-12 | P60422 (AlphaFold model) |
| 50S ribosomal protein L3 | L | protein | 209 | Escherichia coli K-12 | P60438 (AlphaFold model) |
| 50S ribosomal protein L4 | M | protein | 201 | Escherichia coli K-12 | P60723 (AlphaFold model) |
| 50S ribosomal protein L6 | O | protein | 177 | Escherichia coli K-12 | P0AG55 (AlphaFold model) |
| 50S ribosomal protein L13 | R | protein | 142 | Escherichia coli K-12 | P0AA10 |
| 50S ribosomal protein L14 | S | protein | 123 | Escherichia coli K-12 | P0ADY3 |
| 50S ribosomal protein L15 | T | protein | 143 | Escherichia coli K-12 | P02413 |
| 50S ribosomal protein L16 | U | protein | 136 | Escherichia coli K-12 | P0ADY7 |
| 50S ribosomal protein L17 | V | protein | 127 | Escherichia coli K-12 | P0AG44 |
| 50S ribosomal protein L18 | W | protein | 117 | Escherichia coli K-12 | P0C018 |
17 more molecules are not listed.
Sequence of entity 1 (I), FASTA
>7QQ3_1 23S ribosomal RNA (chains I)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCUU
Sequence of entity 2 (J), FASTA
>7QQ3_2 5S ribosomal RNA (chains J)
UGCCUGGCGGCAGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCUCAUGCGAGAGUAGGGAACUGCCAGGCAU
Sequence of entity 3 (K), FASTA
>7QQ3_3 50S ribosomal protein L2 (chains K)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK
Sequence of entity 4 (L), FASTA
>7QQ3_4 50S ribosomal protein L3 (chains L)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 5 (M), FASTA
>7QQ3_5 50S ribosomal protein L4 (chains M)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 6 (O), FASTA
>7QQ3_6 50S ribosomal protein L6 (chains O)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK
Sequence of entity 7 (R), FASTA
>7QQ3_7 50S ribosomal protein L13 (chains R)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI
Sequence of entity 8 (S), FASTA
>7QQ3_8 50S ribosomal protein L14 (chains S)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EVL
Sequence of entity 9 (T), FASTA
>7QQ3_9 50S ribosomal protein L15 (chains T)
MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRR
LPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPV
TVRGLRVTKGARAAIEAAGGKIE
Sequence of entity 10 (U), FASTA
>7QQ3_10 50S ribosomal protein L16 (chains U)
MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQ
GKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLA
AAKLPIKTTFVTKTVM
Sequence of entity 11 (V), FASTA
>7QQ3_11 50S ribosomal protein L17 (chains V)
MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSV
ANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSE
KAEAAAE
Sequence of entity 12 (W), FASTA
>7QQ3_12 50S ribosomal protein L18 (chains W)
MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAE
QLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
| MG | Magnesium ion | Mg | 145 |
Primary citation
The Myxobacterial Antibiotic Myxovalargin: Biosynthesis, Structural Revision, Total Synthesis, and Molecular Characterization of Ribosomal Inhibition. Koller, T.O., Scheid, U., Kosel, T. et al. J Am Chem Soc (2023) 145:851-863. DOI 10.1021/jacs.2c08816 · 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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