9H8G: Complex 5 30S-GE81112
Complex 5 30S-GE81112. Determined by electron microscopy at 2.09 Å resolution. Released 6 Aug 2025.
- Method
- Electron microscopy
- Resolution
- 2.09 Å
- Organism
- Escherichia coli
- Chains
- 13
- Atoms
- 35,253
- Mol. weight
- 659.06 kDa
- Ligands
- A1IC4, MG
- Released
- 6 Aug 2025
Explore 9H8G in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9H8G contains 57 α-helices and 57 β-strands across 12 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 D: 13 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-15 | 7 | |
| α-helix | 50-65 | 16 | |
| α-helix | 69-81 | 13 | |
| α-helix | 86-96 | 11 | |
| β-strand | 97 | 1 | 1 |
| α-helix | 98-104 | 7 | |
| α-helix | 111-119 | 9 | |
| β-strand | 123-125 | 3 | 2 |
| β-strand | 128-129 | 2 | 2 |
| α-helix | 135 | 1 | |
| β-strand | 136 | 1 | 1 |
| α-helix | 137-138 | 2 | |
| β-strand | 141-145 | 5 | 2 |
| α-helix | 153-161 | 9 | |
| α-helix | 162-164 | 3 | |
| α-helix | 166-168 | 3 | |
| β-strand | 171-174 | 4 | 2 |
| β-strand | 179-182 | 4 | 2 |
| α-helix | 185-187 | 3 | |
| α-helix | 197-205 | 9 | |
Chain E: 5 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-24 | 13 | 3 |
| β-strand | 29-40 | 12 | 3 |
| β-strand | 45-53 | 9 | 3 |
| α-helix | 56-69 | 14 | |
| β-strand | 72-73 | 2 | 3 |
| β-strand | 77 | 1 | 4 |
| β-strand | 80 | 1 | 4 |
| β-strand | 85-89 | 5 | 5 |
| β-strand | 92-98 | 7 | 5 |
| β-strand | 105-106 | 2 | 5 |
| α-helix | 110-118 | 9 | |
| β-strand | 123-129 | 7 | 5 |
| α-helix | 133-146 | 14 | |
| α-helix | 150-156 | 7 | |
| α-helix | 161-164 | 4 | |
Chain F: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-10 | 9 | 6 |
| α-helix | 12-14 | 3 | |
| α-helix | 18-31 | 14 | |
| β-strand | 35-40 | 6 | 6 |
| β-strand | 45-51 | 7 | 7 |
| β-strand | 54-57 | 4 | 7 |
| β-strand | 58-66 | 9 | 6 |
| α-helix | 68-80 | 13 | |
| β-strand | 84-92 | 9 | 6 |
| α-helix | 99-100 | 2 | |
| α-helix | 101-104 | 4 | |
Chain H: 6 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-19 | 14 | |
| β-strand | 24-28 | 5 | 8 |
| α-helix | 31-42 | 12 | |
| β-strand | 46-52 | 7 | 8 |
| α-helix | 57 | 1 | |
| β-strand | 58-63 | 6 | 8 |
| β-strand | 65-66 | 2 | 9 |
| β-strand | 69-70 | 2 | 9 |
| β-strand | 75-77 | 3 | 10 |
| β-strand | 80 | 1 | 11 |
| β-strand | 83 | 1 | 11 |
| β-strand | 86-87 | 2 | 10 |
| α-helix | 89-91 | 3 | |
| α-helix | 95-98 | 4 | |
| β-strand | 101-106 | 6 | 10 |
| β-strand | 109-112 | 4 | 10 |
| α-helix | 113-118 | 6 | |
| β-strand | 123-129 | 7 | 10 |
Chain K: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-25 | 8 | 12 |
| β-strand | 30-36 | 7 | 12 |
| β-strand | 41-46 | 6 | 12 |
| α-helix | 55-58 | 4 | |
| α-helix | 60-73 | 14 | |
| β-strand | 81-87 | 7 | 12 |
| α-helix | 95-103 | 9 | |
| β-strand | 106-112 | 7 | 12 |
| α-helix | 122-127 | 6 | |
Chain L: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 22-24 | 3 | |
| β-strand | 29-40 | 12 | 13 |
| β-strand | 50-57 | 8 | 13 |
| β-strand | 62-66 | 5 | 13 |
| β-strand | 79-84 | 6 | 13 |
| β-strand | 95-97 | 3 | 13 |
| α-helix | 104-107 | 4 | |
| α-helix | 114-116 | 3 | |
| α-helix | 120-123 | 4 | |
Chain O: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 25-45 | 21 | |
| α-helix | 50-73 | 24 | |
| α-helix | 75-85 | 11 | |
Chain P: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-11 | 10 | 14 |
| β-strand | 14-23 | 10 | 14 |
| β-strand | 34-39 | 6 | 14 |
| β-strand | 50-52 | 3 | 14 |
| α-helix | 54-62 | 9 | |
| β-strand | 66-67 | 2 | 14 |
| α-helix | 69-81 | 13 | |
4 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 fragment (1078-MER) | A | RNA | 1541 | Escherichia coli | |
| Small ribosomal subunit protein uS4 | D | protein | 206 | Escherichia coli | P0A7V8 (AlphaFold model) |
| Small ribosomal subunit protein uS5 | E | protein | 167 | Escherichia coli | P0A7W1 (AlphaFold model) |
| Small ribosomal subunit protein bS6, fully modified isoform | F | protein | 135 | Escherichia coli | P02358 (AlphaFold model) |
| Small ribosomal subunit protein uS8 | H | protein | 130 | Escherichia coli | P0A7W7 (AlphaFold model) |
| Small ribosomal subunit protein uS11 | K | protein | 129 | Escherichia coli | P0A7R9 |
| Small ribosomal subunit protein uS12 | L | protein | 124 | Escherichia coli | P0A7S3 |
| Small ribosomal subunit protein uS15 | O | protein | 89 | Escherichia coli | P0ADZ4 |
| Small ribosomal subunit protein bS16 | P | protein | 82 | Escherichia coli | P0A7T3 |
| Small ribosomal subunit protein uS17 | Q | protein | 84 | Escherichia coli | P0AG63 |
| Small ribosomal subunit protein bS18 | R | protein | 75 | Escherichia coli | P0A7T7 |
| Small ribosomal subunit protein bS20 | T | protein | 87 | Escherichia coli | P0A7U7 |
1 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>9H8G_1 16S rRNA fragment (1078-MER) (chains A)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUA
GCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAAC
AAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA
Sequence of entity 2 (D), FASTA
>9H8G_2 Small ribosomal subunit protein uS4 (chains D)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK
Sequence of entity 3 (E), FASTA
>9H8G_3 Small ribosomal subunit protein uS5 (chains E)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK
Sequence of entity 4 (F), FASTA
>9H8G_4 Small ribosomal subunit protein bS6, fully modified isoform (chains F)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE
Sequence of entity 5 (H), FASTA
>9H8G_5 Small ribosomal subunit protein uS8 (chains H)
MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELE
LTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAG
LGGEIICYVA
Sequence of entity 6 (K), FASTA
>9H8G_6 Small ribosomal subunit protein uS11 (chains K)
MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTP
FAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNG
CRPPKKRRV
Sequence of entity 7 (L), FASTA
>9H8G_7 Small ribosomal subunit protein uS12 (chains L)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA
Sequence of entity 8 (O), FASTA
>9H8G_8 Small ribosomal subunit protein uS15 (chains O)
MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMV
SQRRKLLDYLKRKDVARYTQLIERLGLRR
Sequence of entity 9 (P), FASTA
>9H8G_9 Small ribosomal subunit protein bS16 (chains P)
MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHW
VGQGATISDRVAALIKEVNKAA
Sequence of entity 10 (Q), FASTA
>9H8G_10 Small ribosomal subunit protein uS17 (chains Q)
MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVE
IRECRPLSKTKSWTLVRVVEKAVL
Sequence of entity 11 (R), FASTA
>9H8G_11 Small ribosomal subunit protein bS18 (chains R)
MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIK
RARYLSLLPYTDRHQ
Sequence of entity 12 (T), FASTA
>9H8G_12 Small ribosomal subunit protein bS20 (chains T)
MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDR
QAAKGLIHKNKAARHKANLTAQINKLA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| A1IC4 | (2S,3S)-2-[[(2S)-2-[[(2S,4S)-5-aminocarbonyloxy-4-oxidanyl-2-[[(2S,3R)-3-oxidan… | C24 H34 Cl N9 O10 | 1 |
| MG | Magnesium ion | Mg | 99 |
Water and common crystallization additives (K) are not listed.
Primary citation
A binding site for the antibiotic GE81112 in the ribosomal mRNA channel. Schedlbauer, A., Han, X., van Bakel, W. et al. bioRxiv (2024). DOI 10.1101/2024.09.26.614503 · PubMed
Other PDB entries of the same protein (UniProt P0A7V8 (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…
- 8CGJ 1.79 Å, Streptomycin bound to the 30S body
- 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
- 9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
- 8CGU 1.89 Å, Gentamicin bound to the 30S body
- 9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
- 8AYE 1.96 Å, E. coli 70S ribosome bound to thermorubin and fMet-tRNA
- 7K00 1.98 Å, Structure of the Bacterial Ribosome at 2 Angstrom Resolution
- 9Q3R 1.99 Å, Cryo-EM structure of the Escherichia coli 70S ribosome bound to mRNA, P-site…
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