7OJ0: 70S ribosome stalled with TnaC peptide and RF2
Cryo-EM structure of 70S ribosome stalled with TnaC peptide and RF2. Determined by electron microscopy at 3.5 Å resolution. Released 15 Sept 2021.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organisms
- Escherichia coli K-12, Escherichia coli (strain K12)
- Chains
- 59
- Atoms
- 146,507
- Mol. weight
- 2211.43 kDa
- Ligands
- MG, TRP, ZN
- Released
- 15 Sept 2021
Explore 7OJ0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7OJ0 contains 251 α-helices and 308 β-strands across 54 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: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-13 | 7 | 77 |
| β-strand | 20-25 | 6 | 77 |
| β-strand | 35-40 | 6 | 77 |
| β-strand | 45-52 | 8 | 77 |
Chain 1: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-15 | 7 | |
| α-helix | 18-23 | 6 | |
| α-helix | 25-37 | 13 | |
Chain 2: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 8-13 | 6 | |
| β-strand | 15-16 | 2 | 87 |
| β-strand | 22-24 | 3 | 87 |
| α-helix | 38-44 | 7 | |
| β-strand | 48-49 | 2 | 87 |
| α-helix | 52-61 | 10 | |
Chain 3: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 90 |
| β-strand | 14-19 | 6 | 90 |
| β-strand | 22-27 | 6 | 90 |
| α-helix | 31-33 | 3 | |
| β-strand | 35-37 | 3 | 90 |
Chain 4: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-8 | 2 | |
| β-strand | 10-16 | 7 | 93 |
| β-strand | 20-26 | 7 | 93 |
| β-strand | 32-34 | 3 | 93 |
| α-helix | 42-45 | 4 | |
| α-helix | 56-63 | 8 | |
Chain 5: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-20 | 17 | |
| β-strand | 23-27 | 5 | 32 |
| α-helix | 34-47 | 14 | |
| α-helix | 63-66 | 4 | |
| α-helix | 67-69 | 3 | |
| α-helix | 72-75 | 4 | |
| β-strand | 83-87 | 5 | 32 |
| α-helix | 95-104 | 10 | |
Chain 6: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4 | 1 | 50 |
| α-helix | 15-20 | 6 | |
| α-helix | 23-25 | 3 | |
| β-strand | 28 | 1 | 18 |
Chain 7: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-15 | 4 | |
46 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 |
|---|
| 16S rRNA | A | RNA | 1519 | Escherichia coli K-12 | |
| 30S ribosomal protein S2 | B | protein | 241 | Escherichia coli (strain K12) | P0A7V0 (AlphaFold model) |
| 30S ribosomal protein S3 | C | protein | 233 | Escherichia coli (strain K12) | P0A7V3 (AlphaFold model) |
| 30S ribosomal protein S4 | D | protein | 206 | Escherichia coli (strain K12) | P0A7V8 (AlphaFold model) |
| 30S ribosomal protein S5 | E | protein | 167 | Escherichia coli (strain K12) | P0A7W1 (AlphaFold model) |
| 30S ribosomal protein S6, fully modified isoform | F | protein | 135 | Escherichia coli (strain K12) | P02358 |
| 30S ribosomal protein S7 | G | protein | 179 | Escherichia coli (strain K12) | P02359 |
| 30S ribosomal protein S8 | H | protein | 130 | Escherichia coli (strain K12) | P0A7W7 |
| 30S ribosomal protein S9 | I | protein | 130 | Escherichia coli (strain K12) | P0A7X3 |
| 30S ribosomal protein S10 | J | protein | 103 | Escherichia coli (strain K12) | P0A7R5 |
| 30S ribosomal protein S11 | K | protein | 129 | Escherichia coli (strain K12) | P0A7R9 |
| 30S ribosomal protein S12 | L | protein | 124 | Escherichia coli (strain K12) | P0A7S3 |
47 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>7OJ0_1 16S rRNA (chains A)
AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAG
UCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAU
GUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUA
ACGUCGCAAGACCAAAGAGGGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUA
GUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAG
CCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGC
ACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUA
AAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCC
GCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCG
UUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAU
CCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGG
GUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAG
GCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUA
GAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCGGCGUGGCUU
CCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAA
UGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAA
GAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGA
ACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGU
CCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGA
GACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACG
ACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAA
GCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGU
CGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUAC
ACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGG
AGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGG
GGAACCUGCGGUUGGAUCA
Sequence of entity 2 (B), FASTA
>7OJ0_2 30S ribosomal protein S2 (chains B)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E
Sequence of entity 3 (C), FASTA
>7OJ0_3 30S ribosomal protein S3 (chains C)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK
Sequence of entity 4 (D), FASTA
>7OJ0_4 30S ribosomal protein S4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK
Sequence of entity 5 (E), FASTA
>7OJ0_5 30S ribosomal protein S5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK
Sequence of entity 6 (F), FASTA
>7OJ0_6 30S ribosomal protein S6, fully modified isoform (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE
Sequence of entity 7 (G), FASTA
>7OJ0_7 30S ribosomal protein S7 (chains G)
MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELE
AFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN
Sequence of entity 8 (H), FASTA
>7OJ0_8 30S ribosomal protein S8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA
Sequence of entity 9 (I), FASTA
>7OJ0_9 30S ribosomal protein S9 (chains I)
MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEK
LDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRK
ARRRPQFSKR
Sequence of entity 10 (J), FASTA
>7OJ0_10 30S ribosomal protein S10 (chains J)
MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKD
ARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG
Sequence of entity 11 (K), FASTA
>7OJ0_11 30S ribosomal protein S11 (chains K)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHDG
CRPPKKRRV
Sequence of entity 12 (L), FASTA
>7OJ0_12 30S ribosomal protein S12 (chains L)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 308 |
| TRP | Tryptophan | C11 H12 N2 O2 | 1 |
| ZN | Zinc ion | Zn | 2 |
Primary citation
Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide. Su, T., Kudva, R., Becker, T. et al. Nucleic Acids Res (2021) 49:9539-9547. DOI 10.1093/nar/gkab665 · PubMed
Other PDB entries of the same protein (UniProt P0A7V0 (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…
- 4ODN 1.6 Å, Structure of SlyD from Thermus thermophilus in complex with S2-plus peptide
- 7OXH 1.7 Å, ttSlyD with pseudo-wild-type S2 peptide
- 4ODP 1.75 Å, Structure of SlyD delta-IF from Thermus thermophilus in complex with S2-W23A peptide
- 4ODM 1.75 Å, Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide
- 8CGJ 1.79 Å, Streptomycin bound to the 30S body
- 8CF1 1.82 Å, Tetracycline bound to the 30S head
- 7OXJ 1.85 Å, ttSlyD with M8A pseudo-wild-type S2 peptide
- 8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
- 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
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