9FY1: Large ribosomal subunit protein bL32
Structure of CliM-stalled Bacillus subtilis 70S ribosome with release factor bound in the A-site. Determined by electron microscopy at 2.3 Å resolution. Released 14 Jan 2026.
- Method
- Electron microscopy
- Resolution
- 2.3 Å
- Organisms
- Bacillus subtilis subsp. subtilis str. 168, Clostridioides difficile 630
- Chains
- 53
- Atoms
- 138,648
- Mol. weight
- 2182.18 kDa
- Ligands
- ZN
- Released
- 14 Jan 2026
Explore 9FY1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9FY1 contains 250 α-helices and 338 β-strands across 48 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, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| α-helix | 10-16 | 7 | |
| α-helix | 17-19 | 3 | |
| β-strand | 27-29 | 3 | 1 |
| β-strand | 36-38 | 3 | 1 |
| β-strand | 41 | 1 | 2 |
| β-strand | 43 | 1 | 3 |
| β-strand | 48 | 1 | 3 |
Chain 1: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 12 |
| β-strand | 15-21 | 7 | 12 |
| β-strand | 31-36 | 6 | 12 |
| β-strand | 41-47 | 7 | 12 |
Chain 2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-37 | 13 | |
Chain 3: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 8-13 | 6 | |
| β-strand | 15-16 | 2 | 14 |
| β-strand | 22-24 | 3 | 14 |
| α-helix | 33-35 | 3 | |
| α-helix | 38-45 | 8 | |
| β-strand | 48-49 | 2 | 14 |
| α-helix | 52-58 | 7 | |
| α-helix | 59-62 | 4 | |
Chain 4: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 19 |
| β-strand | 15-19 | 5 | 19 |
| β-strand | 22-26 | 5 | 19 |
| α-helix | 30-32 | 3 | |
| β-strand | 34-35 | 2 | 19 |
Chain 5: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 82 | 1 | 23 |
| α-helix | 86-92 | 7 | |
| α-helix | 96-99 | 4 | |
| α-helix | 101-104 | 4 | |
| α-helix | 108-111 | 4 | |
Chain 6: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-8 | 2 | |
| β-strand | 10-11 | 2 | 25 |
| β-strand | 14-16 | 3 | 26 |
| β-strand | 21-22 | 2 | 26 |
| β-strand | 25-26 | 2 | 25 |
| β-strand | 31-33 | 3 | 26 |
| α-helix | 41-44 | 4 | |
Chain 8: 9 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 126 | 1 | |
| β-strand | 127-133 | 7 | 103 |
| α-helix | 138-156 | 19 | |
| β-strand | 161-169 | 9 | 103 |
| β-strand | 175-183 | 9 | 103 |
| α-helix | 188-191 | 4 | |
| α-helix | 192-194 | 3 | |
| β-strand | 196-203 | 8 | 103 |
| β-strand | 212-214 | 3 | 103 |
| β-strand | 217-223 | 7 | 103 |
| β-strand | 238-243 | 6 | 104 |
| α-helix | 252-255 | 4 | |
| β-strand | 259-264 | 6 | 104 |
| β-strand | 269-273 | 5 | 104 |
| α-helix | 279-309 | 31 | |
| α-helix | 313-315 | 3 | |
| β-strand | 321-326 | 6 | 103 |
| β-strand | 335 | 1 | 103 |
| α-helix | 345-350 | 6 | |
| α-helix | 355-365 | 11 | |
40 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 | 59 | Bacillus subtilis subsp. subtilis str. 168 | O34687 (AlphaFold model) |
| 50S ribosomal protein L33 1 | 1 | protein | 49 | Bacillus subtilis subsp. subtilis str. 168 | P56849 (AlphaFold model) |
| 50S ribosomal protein L34 | 2 | protein | 44 | Bacillus subtilis subsp. subtilis str. 168 | P05647 (AlphaFold model) |
| 50S ribosomal protein L35 | 3 | protein | 66 | Bacillus subtilis subsp. subtilis str. 168 | P55874 (AlphaFold model) |
| 50S ribosomal protein L36 | 4 | protein | 37 | Bacillus subtilis subsp. subtilis str. 168 | P20278 |
| Nascent Chain CliM | 5 | protein | 38 | Clostridioides difficile 630 | A0A9Q7T0I1 |
| 50S ribosomal protein L31 | 6 | protein | 66 | Bacillus subtilis subsp. subtilis str. 168 | Q03223 |
| mRNA | 7 | RNA | 9 | Clostridioides difficile 630 | |
| 5S rRNA | B | RNA | 112 | Bacillus subtilis subsp. subtilis str. 168 | |
| Large ribosomal subunit protein uL2 | C | protein | 277 | Bacillus subtilis subsp. subtilis str. 168 | P42919 |
| 50S ribosomal protein L3 | D | protein | 209 | Bacillus subtilis subsp. subtilis str. 168 | P42920 |
| 50S ribosomal protein L4 | E | protein | 207 | Bacillus subtilis subsp. subtilis str. 168 | P42921 |
41 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>9FY1_1 Large ribosomal subunit protein bL32 (chains 0)
MAVPFRRTSKVKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNGKDINVKSN
Sequence of entity 2 (1), FASTA
>9FY1_2 50S ribosomal protein L33 1 (chains 1)
MRVNITLACTECGERNYISKKNKRNNPDRVEFKKYCPRDKKSTLHRETK
Sequence of entity 3 (2), FASTA
>9FY1_3 50S ribosomal protein L34 (chains 2)
MKRTFQPNNRKRSKVHGFRSRMSSKNGRLVLARRRRKGRKVLSA
Sequence of entity 4 (3), FASTA
>9FY1_4 50S ribosomal protein L35 (chains 3)
MPKMKTHRGSAKRFKKTGSGKLKRSHAYTSHLFANKSQKQKRKLRKSAVVSAGDFKRIKQ
MLANIK
Sequence of entity 5 (4), FASTA
>9FY1_5 50S ribosomal protein L36 (chains 4)
MKVRPSVKPICEKCKVIRRKGKVMVICENPKHKQKQG
Sequence of entity 6 (5), FASTA
>9FY1_6 Nascent Chain CliM (chains 5)
YVLIRDIFVNRITYSEERLPKQYIVFQKYDIWRYCSLF
Sequence of entity 7 (6), FASTA
>9FY1_7 50S ribosomal protein L31 (chains 6)
MKAGIHPNFKKATVKCACGNEFETGSVKEEVRVEICSECHPFYTGRQKFASADGRVDRFN
KKYGLK
Sequence of entity 8 (7), FASTA
>9FY1_8 mRNA (chains 7)
UUGUUUUAA
Sequence of entity 9 (B), FASTA
>9FY1_9 5S rRNA (chains B)
UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUU
CAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA
Sequence of entity 10 (C), FASTA
>9FY1_10 Large ribosomal subunit protein uL2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGVRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK
Sequence of entity 11 (D), FASTA
>9FY1_11 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK
Sequence of entity 12 (E), FASTA
>9FY1_12 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Diverse mechanisms of translation arrest by a Clostridia ribosome stalling peptide CliM. Yoshida, M., Gersteuer, F., Berendes, O. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-72673-5 · PubMed
Other PDB entries of the same protein (UniProt O34687 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8S1P 1.96 Å, YlmH bound to PtRNA-50S
- 8QCQ 2.3 Å, B. subtilis ApdA-stalled ribosomal complex
- 9FY2 2.3 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-site
- 9FY3 2.8 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-site
- 7AS8 2.9 Å, Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with…
- 8BUU 2.9 Å, ARE-ABCF VmlR2 bound to a 70S ribosome
- 7AQC 2.99 Å, Structure of the bacterial RQC complex (Decoding State)
- 7SAE 3.0 Å, 44SR70P Class1 ribosomal particle
- 6TNN 3.07 Å, Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA
- 6TPQ 3.07 Å, RNase M5 bound to 50S ribosome with precursor 5S rRNA
- 6HA1 3.1 Å, Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader…
- 7AQD 3.1 Å, Structure of the bacterial RQC complex (Translocating State)
Browse structure collections
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