8S1U: YlmH
YlmH bound to stalled 50S subunits with RqcH and PtRNA. Determined by electron microscopy at 3.4 Å resolution. Released 12 Jun 2024.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organism
- Bacillus subtilis subsp. subtilis str. 168
- Chains
- 33
- Atoms
- 93,269
- Mol. weight
- 1476.7 kDa
- Released
- 12 Jun 2024
Explore 8S1U in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8S1U contains 164 α-helices and 255 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: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| α-helix | 10-16 | 7 | |
| β-strand | 27-29 | 3 | 3 |
| β-strand | 36-38 | 3 | 3 |
| β-strand | 41 | 1 | 4 |
| β-strand | 48 | 1 | 5 |
| β-strand | 53 | 1 | 5 |
Chain 1: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-9 | 8 | 9 |
| β-strand | 17-22 | 6 | 9 |
| β-strand | 31-36 | 6 | 9 |
| β-strand | 41-47 | 7 | 9 |
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: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 8-11 | 4 | |
| β-strand | 15 | 1 | 12 |
| α-helix | 21-22 | 2 | |
| β-strand | 23-25 | 3 | 12 |
| α-helix | 38-44 | 7 | |
| β-strand | 47-49 | 3 | 12 |
| α-helix | 52-58 | 7 | |
| α-helix | 60-62 | 3 | |
Chain 4: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 13 |
| β-strand | 15-18 | 4 | 13 |
| β-strand | 23-26 | 4 | 13 |
| β-strand | 34-36 | 3 | 13 |
Chain 6: 1 helix, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-16 | 7 | 22 |
| β-strand | 21-26 | 6 | 22 |
| β-strand | 30-33 | 4 | 22 |
| α-helix | 41-44 | 4 | |
Chain C: 11 helices, 31 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 23 |
| α-helix | 6-7 | 2 | |
| β-strand | 17-19 | 3 | 23 |
| α-helix | 29-30 | 2 | |
| α-helix | 31-33 | 3 | |
| β-strand | 34-35 | 2 | 24 |
| β-strand | 43 | 1 | 25 |
| β-strand | 49 | 1 | 25 |
| β-strand | 54 | 1 | 26 |
| α-helix | 61 | 1 | |
| β-strand | 62-63 | 2 | 24 |
| β-strand | 65 | 1 | 27 |
| β-strand | 72 | 1 | 28 |
| β-strand | 75-78 | 4 | 27 |
| β-strand | 82 | 1 | 27 |
| β-strand | 91-96 | 6 | 27 |
| β-strand | 101-105 | 5 | 27 |
| β-strand | 107 | 1 | 29 |
| β-strand | 115-117 | 3 | 27 |
| β-strand | 118 | 1 | 28 |
| β-strand | 126 | 1 | 30 |
| β-strand | 128 | 1 | 30 |
| β-strand | 129-131 | 3 | 28 |
| α-helix | 136 | 1 | |
| β-strand | 140-142 | 3 | 28 |
| β-strand | 144 | 1 | 31 |
| β-strand | 154 | 1 | 31 |
| β-strand | 162-168 | 7 | 28 |
| β-strand | 171-175 | 5 | 28 |
| β-strand | 181-185 | 5 | 28 |
| β-strand | 189-192 | 4 | 28 |
| α-helix | 194 | 1 | |
| β-strand | 195 | 1 | 29 |
| α-helix | 198-202 | 5 | |
| α-helix | 208-213 | 6 | |
| β-strand | 216 | 1 | 26 |
| α-helix | 222-224 | 3 | |
| α-helix | 227-229 | 3 | |
| β-strand | 247 | 1 | 32 |
| β-strand | 253 | 1 | 32 |
| α-helix | 266-268 | 3 | |
| β-strand | 270-272 | 3 | 28 |
Chain D: 7 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-16 | 13 | 33 |
| β-strand | 22-29 | 8 | 33 |
| β-strand | 33-39 | 7 | 34 |
| β-strand | 48-55 | 8 | 34 |
| α-helix | 56-57 | 2 | |
| α-helix | 63-69 | 7 | |
| β-strand | 77-84 | 8 | 34 |
| α-helix | 88-90 | 3 | |
| β-strand | 96-97 | 2 | 34 |
| α-helix | 99-101 | 3 | |
| β-strand | 107-113 | 7 | 33 |
| α-helix | 114-116 | 3 | |
| β-strand | 118-120 | 3 | 35 |
| α-helix | 122-126 | 5 | |
| α-helix | 128-130 | 3 | |
| β-strand | 162-164 | 3 | 35 |
| β-strand | 168-180 | 13 | 33 |
| β-strand | 185-189 | 5 | 33 |
| β-strand | 199-204 | 6 | 33 |
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 |
|---|
| P-tRNA | a, c | RNA | 76 | Bacillus subtilis subsp. subtilis str. 168 | |
| 50S ribosomal protein L32 | 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 |
| 50S ribosomal protein L31 | 6 | protein | 66 | Bacillus subtilis subsp. subtilis str. 168 | Q03223 |
| 5S rRNA | B | RNA | 112 | Bacillus subtilis subsp. subtilis str. 168 | |
| 50S ribosomal protein L2 | 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 |
| 50S ribosomal protein L5 | F | protein | 179 | Bacillus subtilis subsp. subtilis str. 168 | P12877 |
20 more molecules are not listed.
Sequence of entity 1 (a, c), FASTA
>8S1U_1 P-tRNA (chains a, c)
GGGGCCUUAGCUCAGCUGGGAGAGCGCCUGCUUUGCACGCAGGAGGUCAGCGGUUCGAUC
CCGCUAGGCUCCACCA
Sequence of entity 2 (0), FASTA
>8S1U_2 50S ribosomal protein L32 (chains 0)
MAVPFRRTSKMKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNGKDINVKSN
Sequence of entity 3 (1), FASTA
>8S1U_3 50S ribosomal protein L33 1 (chains 1)
MRVNITLACTECGERNYISKKNKRNNPDRVEFKKYCPRDKKSTLHRETK
Sequence of entity 4 (2), FASTA
>8S1U_4 50S ribosomal protein L34 (chains 2)
MKRTFQPNNRKRSKVHGFRSRMSSKNGRLVLARRRRKGRKVLSA
Sequence of entity 5 (3), FASTA
>8S1U_5 50S ribosomal protein L35 (chains 3)
MPKMKTHRGSAKRFKKTGSGKLKRSHAYTSHLFANKSQKQKRKLRKSAVVSAGDFKRIKQ
MLANIK
Sequence of entity 6 (4), FASTA
>8S1U_6 50S ribosomal protein L36 (chains 4)
MKVRPSVKPICEKCKVIRRKGKVMVICENPKHKQKQG
Sequence of entity 7 (6), FASTA
>8S1U_7 50S ribosomal protein L31 (chains 6)
MKAGIHPNFKKATVKCACGNEFETGSVKEEVRVEICSECHPFYTGRQKFASADGRVDRFN
KKYGLK
Sequence of entity 8 (B), FASTA
>8S1U_8 5S rRNA (chains B)
UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUU
CAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA
Sequence of entity 9 (C), FASTA
>8S1U_9 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK
Sequence of entity 10 (D), FASTA
>8S1U_10 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK
Sequence of entity 11 (E), FASTA
>8S1U_11 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA
Sequence of entity 12 (F), FASTA
>8S1U_12 50S ribosomal protein L5 (chains F)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK
Primary citation
A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis. Takada, H., Paternoga, H., Fujiwara, K. et al. Nucleic Acids Res (2024) 52:8483-8499. DOI 10.1093/nar/gkae399 · 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
- 9FY1 2.3 Å, Structure of CliM-stalled Bacillus subtilis 70S ribosome with release factor bound in…
- 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…
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