8RPZ: Escherichia coli 50S subunit
Escherichia coli 50S subunit in complex with the antimicrobial peptide Api88 - conformation I. Determined by electron microscopy at 2.44 Å resolution. Released 22 May 2024.
- Method
- Electron microscopy
- Resolution
- 2.44 Å
- Organisms
- Escherichia coli, Apis mellifera
- Chains
- 34
- Atoms
- 90,661
- Mol. weight
- 1351.19 kDa
- Released
- 22 May 2024
Explore 8RPZ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8RPZ contains 122 α-helices and 202 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 0: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| α-helix | 9-16 | 8 | |
| α-helix | 17-19 | 3 | |
| β-strand | 27-29 | 3 | 1 |
| β-strand | 36-38 | 3 | 1 |
| β-strand | 47-48 | 2 | 2 |
| β-strand | 51-52 | 2 | 2 |
Chain 1: 0 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-12 | 7 | 4 |
| β-strand | 19-24 | 6 | 4 |
| β-strand | 36-39 | 4 | 5 |
| β-strand | 44-47 | 4 | 5 |
| β-strand | 48-51 | 4 | 4 |
Chain 2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-23 | 6 | |
| α-helix | 25-37 | 13 | |
Chain 3: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 7-10 | 4 | |
| β-strand | 14-15 | 2 | 10 |
| β-strand | 21-23 | 3 | 10 |
| α-helix | 37-43 | 7 | |
| β-strand | 47-48 | 2 | 10 |
| α-helix | 49-50 | 2 | |
| α-helix | 54-60 | 7 | |
Chain 4: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 11 |
| β-strand | 14-19 | 6 | 11 |
| β-strand | 22-27 | 6 | 11 |
| α-helix | 31-33 | 3 | |
| β-strand | 35 | 1 | 11 |
Chain 6: 0 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-15 | 5 | 13 |
| β-strand | 21-25 | 5 | 13 |
| β-strand | 33 | 1 | 13 |
Chain C: 7 helices, 26 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 14 |
| α-helix | 5-6 | 2 | |
| β-strand | 16-18 | 3 | 14 |
| β-strand | 23 | 1 | 15 |
| α-helix | 30-32 | 3 | |
| β-strand | 33-34 | 2 | 16 |
| β-strand | 42 | 1 | 17 |
| β-strand | 48 | 1 | 17 |
| β-strand | 53 | 1 | 18 |
| α-helix | 60 | 1 | |
| β-strand | 61-62 | 2 | 16 |
| β-strand | 64 | 1 | 15 |
| β-strand | 75-81 | 7 | 15 |
| β-strand | 90-95 | 6 | 15 |
| β-strand | 100-104 | 5 | 15 |
| β-strand | 106 | 1 | 19 |
| β-strand | 114-115 | 2 | 15 |
| β-strand | 117 | 1 | 20 |
| β-strand | 128-130 | 3 | 20 |
| α-helix | 135 | 1 | |
| β-strand | 139-141 | 3 | 20 |
| β-strand | 143 | 1 | 21 |
| β-strand | 153 | 1 | 21 |
| β-strand | 161-167 | 7 | 20 |
| β-strand | 170-174 | 5 | 20 |
| β-strand | 180-184 | 5 | 20 |
| β-strand | 188-191 | 4 | 20 |
| β-strand | 194 | 1 | 19 |
| α-helix | 197-201 | 5 | |
| α-helix | 207-211 | 5 | |
| β-strand | 215 | 1 | 18 |
| α-helix | 263-265 | 3 | |
| β-strand | 266-268 | 3 | 20 |
Chain D: 8 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-15 | 12 | 22 |
| β-strand | 21-28 | 8 | 22 |
| α-helix | 31 | 1 | |
| β-strand | 32-38 | 7 | 23 |
| α-helix | 40-43 | 4 | |
| β-strand | 47-52 | 6 | 23 |
| α-helix | 62-71 | 10 | |
| β-strand | 77-83 | 7 | 23 |
| β-strand | 95-96 | 2 | 23 |
| α-helix | 98-101 | 4 | |
| β-strand | 106-112 | 7 | 22 |
| α-helix | 113-115 | 3 | |
| β-strand | 117-119 | 3 | 24 |
| α-helix | 121-125 | 5 | |
| α-helix | 127-129 | 3 | |
| α-helix | 155-156 | 2 | |
| β-strand | 163-165 | 3 | 24 |
| β-strand | 169-181 | 13 | 22 |
| β-strand | 186-190 | 5 | 22 |
| β-strand | 200-205 | 6 | 22 |
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 |
|---|
| Large ribosomal subunit protein bL32 | 0 | protein | 56 | Escherichia coli | P0A7N4 (AlphaFold model) |
| Large ribosomal subunit protein bL33 | 1 | protein | 50 | Escherichia coli | P0A7N9 (AlphaFold model) |
| Large ribosomal subunit protein bL34 | 2 | protein | 46 | Escherichia coli | P0A7P5 (AlphaFold model) |
| Large ribosomal subunit protein bL35 | 3 | protein | 64 | Escherichia coli | P0A7Q1 (AlphaFold model) |
| Large ribosomal subunit protein bL36A | 4 | protein | 38 | Escherichia coli | P0A7Q6 |
| Large ribosomal subunit protein bL31 | 6 | protein | 66 | Escherichia coli | P0A7M9 |
| 23S ribosomal RNA | A | RNA | 2903 | Escherichia coli | |
| 5S ribosomal RNA | B | RNA | 120 | Escherichia coli | |
| Large ribosomal subunit protein uL2 | C | protein | 271 | Escherichia coli | P60422 |
| Large ribosomal subunit protein uL3 | D | protein | 209 | Escherichia coli | P60438 |
| Large ribosomal subunit protein uL4 | E | protein | 201 | Escherichia coli | P60723 |
| Large ribosomal subunit protein uL5 | F | protein | 177 | Escherichia coli | P62399 |
20 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>8RPZ_1 Large ribosomal subunit protein bL32 (chains 0)
AVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK
Sequence of entity 2 (1), FASTA
>8RPZ_2 Large ribosomal subunit protein bL33 (chains 1)
GIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAK
Sequence of entity 3 (2), FASTA
>8RPZ_3 Large ribosomal subunit protein bL34 (chains 2)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK
Sequence of entity 4 (3), FASTA
>8RPZ_4 Large ribosomal subunit protein bL35 (chains 3)
PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIAC
LPYA
Sequence of entity 5 (4), FASTA
>8RPZ_5 Large ribosomal subunit protein bL36A (chains 4)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG
Sequence of entity 6 (6), FASTA
>8RPZ_6 Large ribosomal subunit protein bL31 (chains 6)
MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRF
NKRFNI
Sequence of entity 7 (A), FASTA
>8RPZ_7 23S ribosomal RNA (chains A)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUCGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGGAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCU
Sequence of entity 8 (B), FASTA
>8RPZ_8 5S ribosomal RNA (chains B)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAA
Sequence of entity 9 (C), FASTA
>8RPZ_9 Large ribosomal subunit protein uL2 (chains C)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS
Sequence of entity 10 (D), FASTA
>8RPZ_10 Large ribosomal subunit protein uL3 (chains D)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 11 (E), FASTA
>8RPZ_11 Large ribosomal subunit protein uL4 (chains E)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 12 (F), FASTA
>8RPZ_12 Large ribosomal subunit protein uL5 (chains F)
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAIS
GQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKS
FDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR
Primary citation
Multimodal binding and inhibition of bacterial ribosomes by the antimicrobial peptides Api137 and Api88. Lauer, S.M., Reepmeyer, M., Berendes, O. et al. Nat Commun (2024) 15:3945-3945. DOI 10.1038/s41467-024-48027-4 · PubMed
Other PDB entries of the same protein (UniProt P0A7N4 (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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