8VTX: 50S ribosomal protein L2
Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with macrolone MCX-128, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution. Determined by X-ray diffraction at 2.4 Å resolution. Released 7 Aug 2024.
- Method
- X-ray diffraction
- Resolution
- 2.4 Å
- Organisms
- Thermus thermophilus HB8, Escherichia phage T4, Escherichia coli
- Chains
- 112
- Atoms
- 300,319
- Mol. weight
- 4571.69 kDa
- Ligands
- MG, A1AE1, ZN, SF4
- Released
- 7 Aug 2024
Explore 8VTX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8VTX contains 499 α-helices and 645 β-strands across 98 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 10: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| β-strand | 22-23 | 2 | 174 |
| β-strand | 30-31 | 2 | 175 |
| β-strand | 36-39 | 4 | 174 |
| β-strand | 46-47 | 2 | 175 |
| β-strand | 51-53 | 3 | 174 |
| β-strand | 59-61 | 3 | 174 |
| β-strand | 65-71 | 7 | 175 |
| α-helix | 73-75 | 3 | |
| β-strand | 77-83 | 7 | 175 |
Chain 11: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-21 | 9 | 180 |
| α-helix | 25-27 | 3 | |
| β-strand | 33-42 | 10 | 180 |
| β-strand | 46-53 | 8 | 181 |
| β-strand | 56-63 | 8 | 181 |
| α-helix | 64-66 | 3 | |
| α-helix | 67-76 | 10 | |
| α-helix | 87-96 | 10 | |
Chain 12: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-14 | 12 | |
| α-helix | 18-40 | 23 | |
| α-helix | 48-67 | 20 | |
Chains 13 and 23: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-8 | 6 | 194 |
| α-helix | 17-25 | 9 | |
| β-strand | 34-38 | 5 | 194 |
| α-helix | 41-49 | 9 | |
| α-helix | 51-53 | 3 | |
| β-strand | 54-59 | 6 | 194 |
Chain 14: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| β-strand | 10-15 | 6 | 201 |
| β-strand | 21-26 | 6 | 201 |
| β-strand | 30-32 | 3 | 201 |
| α-helix | 59-61 | 3 | |
Chain 15: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-12 | 3 | |
| α-helix | 13-19 | 7 | |
| α-helix | 20-22 | 3 | |
| α-helix | 24-29 | 6 | |
| β-strand | 31-32 | 2 | 1 |
| β-strand | 39-40 | 2 | 1 |
| β-strand | 51-52 | 2 | 2 |
| β-strand | 55-56 | 2 | 2 |
Chains 16 and 26: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-13 | 8 | 6 |
| β-strand | 19-26 | 8 | 6 |
| α-helix | 33-34 | 2 | |
| β-strand | 35-40 | 6 | 6 |
| β-strand | 45-53 | 9 | 6 |
Chain 17: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-36 | 12 | |
85 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 | 1A, 2A | RNA | 2915 | Thermus thermophilus HB8 | |
| 5S Ribosomal RNA | 1B, 2B | RNA | 121 | Thermus thermophilus HB8 | |
| 50S ribosomal protein L2 | 1D, 2D | protein | 276 | Thermus thermophilus HB8 | P60405 (AlphaFold model) |
| 50S ribosomal protein L3 | 1E, 2E | protein | 206 | Thermus thermophilus HB8 | Q5SHN8 (AlphaFold model) |
| 50S ribosomal protein L4 | 1F, 2F | protein | 210 | Thermus thermophilus HB8 | Q5SHN9 (AlphaFold model) |
| 50S ribosomal protein L5 | 1G, 2G | protein | 182 | Thermus thermophilus HB8 | Q5SHQ0 (AlphaFold model) |
| 50S ribosomal protein L6 | 1H, 2H | protein | 180 | Thermus thermophilus HB8 | P0DOY8 |
| 50S ribosomal protein L9 | 1I, 2I | protein | 148 | Thermus thermophilus HB8 | Q5SLQ1 |
| 50S ribosomal protein L13 | 1N, 2N | protein | 140 | Thermus thermophilus HB8 | P60488 |
| 50S ribosomal protein L14 | 1O, 2O | protein | 122 | Thermus thermophilus HB8 | Q5SHP8 |
| 50S ribosomal protein L15 | 1P, 2P | protein | 150 | Thermus thermophilus HB8 | Q5SHQ7 |
| 50S ribosomal protein L16 | 1Q, 2Q | protein | 141 | Thermus thermophilus HB8 | P60489 |
44 more molecules are not listed.
Sequence of entity 1 (1A, 2A), FASTA
>8VTX_1 23S Ribosomal RNA (chains 1A, 2A)
GUCAAGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGC
UACCUGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGG
GGAACCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUGCGCGGGGGGAACCUGGGGAAC
UGAAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAG
CGAAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGAC
ACCGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCC
GUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCA
UGGGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCAC
CAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAAC
CGUGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGA
GCCGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCG
AGUCCGAACAGGGCGCAAGCGGGCCGCACGCGGCCCGCAAAGUCCGCGGCCGUGGACCCG
AAACCGGGCGAGCUAGCCCUGGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGA
ACCGGUGGGGGAUGCAAACCCCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAG
CCCGGAGAUAGCUGGUUCUCCCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGG
GCCUGUAGAGCACUGAUAGGGCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCC
GAAGGGUCCCAGGUGGAGCCUGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCG
CGGGAACAACCGAGACCGCCAGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGU
GGCGCCGCGAAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUA
AUAGCUCACUGGUCGAGUGGCGCCGCGCCGAAAAUGAUCGGGGCUUAAGCCCAGCGCCGA
AGCUGCGGGUCUGGGGGAUGACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGG
CCGACCCGCGAGGGCGGCUGGAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAA
AGAGGGUGAGAAUCCCUCUCGCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGU
AGGGUUAGGCGGGACCUAAGGUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUA
UUCCGGCCCUUCCCGCAGGUGCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAU
GGACGAGCCCGGCCAGAAGCGCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAACAAGCUC
UGCGUGGUGGGGAAGCCCGUACGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGC
CUCUAAGCACAACCUGCGGGAACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGA
GCACUCAGGCGCGCGGGAGAACCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUC
GGGAGAAGGGGUGCUCCCUGGGGUGAUGAGCCCCGGGGAGCCGCAGUGAACAGGCUCUGG
CGACUGUUUACCAAAAACACAGCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGAC
GCUUGCCCGGUGCCGGAAGGUCAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUG
AACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCG
ACCUGCACGAAAAGCGUAACGACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGA
ACUGGCCGUGAAGAUGCGGCCUACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACU
GCAGCCUGGUGUUGGCUCUUGGUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCC
CGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAA
CCCUCGGAUGGGGGGACAGCGCUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAA
GGUAACGGAGGCGCCCAAAGGUCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAG
GGUAGAAGGGGGCCUGACUGCGAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAG
UGAACCGGUGGUCCCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAU
AACAGGCUGAUCUCCCCCGAGCGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGG
CUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCG
GCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCA
GGAGGCUUGAGGGGGGCUCUUCCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUU
CCCAGCUGUCCCUCCAGGGGCAUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGA
AAGCAUCUAAGCGGGAAGCCCGCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAG
GACCCGGGAAGACCACCCGGUGGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCC
GACCGGUCCCAAUCGUCCGAGGUCUUGACCCCUCC
Sequence of entity 2 (1B, 2B), FASTA
>8VTX_2 5S Ribosomal RNA (chains 1B, 2B)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
U
Sequence of entity 3 (1D, 2D), FASTA
>8VTX_3 50S ribosomal protein L2 (chains 1D, 2D)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK
Sequence of entity 4 (1E, 2E), FASTA
>8VTX_4 50S ribosomal protein L3 (chains 1E, 2E)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK
Sequence of entity 5 (1F, 2F), FASTA
>8VTX_5 50S ribosomal protein L4 (chains 1F, 2F)
MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS
GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE
GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG
LNVYDIVRTERLVMDLDAWEVFQNRIGGEA
Sequence of entity 6 (1G, 2G), FASTA
>8VTX_6 50S ribosomal protein L5 (chains 1G, 2G)
MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK
Sequence of entity 7 (1H, 2H), FASTA
>8VTX_7 50S ribosomal protein L6 (chains 1H, 2H)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK
Sequence of entity 8 (1I, 2I), FASTA
>8VTX_8 50S ribosomal protein L9 (chains 1I, 2I)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE
Sequence of entity 9 (1N, 2N), FASTA
>8VTX_9 50S ribosomal protein L13 (chains 1N, 2N)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV
Sequence of entity 10 (1O, 2O), FASTA
>8VTX_10 50S ribosomal protein L14 (chains 1O, 2O)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL
Sequence of entity 11 (1P, 2P), FASTA
>8VTX_11 50S ribosomal protein L15 (chains 1P, 2P)
MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLM
RLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAGLLKKGYRLKILGEGEA
KPLKVVAHAFSKSALEKLKAAGGEPVLLEA
Sequence of entity 12 (1Q, 2Q), FASTA
>8VTX_12 50S ribosomal protein L16 (chains 1Q, 2Q)
MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAARVAMVRHFRR
GGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPGRVMFEVAGVTEEQAMEALRI
AGHKLPIKTKIVRRDAYDEAQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 2733 |
| A1AE1 | 1-cyclopropyl-7-(4-{4-[({[(3aR,4R,7R,8S,9S,10R,11R,13R,14E,15S,15aR)-10-{[(2S,3… | C54 H81 F N6 O15 | 2 |
| ZN | Zinc ion | Zn | 12 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
| PHE | Phenylalanine | C9 H11 N O2 | 2 |
| FME | N-formylmethionine | C6 H11 N O3 S | 2 |
Water and common crystallization additives (K) are not listed.
Primary citation
Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms. Aleksandrova, E.V., Ma, C.X., Klepacki, D. et al. Nat Chem Biol (2024) 20:1680-1690. DOI 10.1038/s41589-024-01685-3 · PubMed
Other PDB entries of the same protein (UniProt P60405 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9NO7 2.13 Å, Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 4Y4O 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and…
- 8CVL 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
- 8FC6 2.35 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
- 8VTW 2.35 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 4W2F 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin,…
- 6XHV 2.4 Å, Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex…
- 7RQA 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
- 7RQE 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
- 8CVJ 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
- 8VTU 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 9MTP 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
Browse structure collections
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