9BS0: YphC-treated 45SYphC particle. Class 5
YphC-treated 45SYphC particle. Class 5. Determined by electron microscopy at 3.3 Å resolution. Released 25 Dec 2024.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organism
- Bacillus subtilis subsp. subtilis str. 168
- Chains
- 25
- Atoms
- 81,446
- Mol. weight
- 1345.01 kDa
- Ligands
- GNP
- Released
- 25 Dec 2024
Explore 9BS0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9BS0 contains 105 α-helices and 169 β-strands across 23 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 C: 9 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 1 |
| β-strand | 17-19 | 3 | 1 |
| β-strand | 34-35 | 2 | 2 |
| β-strand | 43 | 1 | 3 |
| β-strand | 49 | 1 | 3 |
| β-strand | 62-63 | 2 | 2 |
| α-helix | 64-65 | 2 | |
| β-strand | 76-82 | 7 | 4 |
| β-strand | 91-96 | 6 | 4 |
| β-strand | 100-105 | 6 | 4 |
| β-strand | 107 | 1 | 5 |
| β-strand | 115-116 | 2 | 4 |
| β-strand | 129-131 | 3 | 6 |
| α-helix | 132-134 | 3 | |
| α-helix | 136 | 1 | |
| β-strand | 141-144 | 4 | 6 |
| β-strand | 154 | 1 | 6 |
| β-strand | 164-168 | 5 | 7 |
| β-strand | 171-176 | 6 | 7 |
| α-helix | 177-179 | 3 | |
| β-strand | 180-184 | 5 | 7 |
| β-strand | 189-192 | 4 | 6 |
| β-strand | 195 | 1 | 5 |
| α-helix | 198-202 | 5 | |
| α-helix | 208-213 | 6 | |
| α-helix | 246 | 1 | |
| β-strand | 247 | 1 | 8 |
| α-helix | 248 | 1 | |
| β-strand | 253 | 1 | 8 |
| α-helix | 265-267 | 3 | |
| β-strand | 270 | 1 | 7 |
Chain D: 8 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-16 | 13 | 9 |
| β-strand | 22-29 | 8 | 9 |
| α-helix | 31-32 | 2 | |
| β-strand | 33-39 | 7 | 10 |
| α-helix | 41-44 | 4 | |
| β-strand | 48-52 | 5 | 10 |
| β-strand | 55 | 1 | 11 |
| α-helix | 63-68 | 6 | |
| α-helix | 75-76 | 2 | |
| β-strand | 77 | 1 | 11 |
| β-strand | 80-84 | 5 | 10 |
| β-strand | 96-97 | 2 | 10 |
| α-helix | 99-101 | 3 | |
| β-strand | 107-113 | 7 | 9 |
| α-helix | 114-116 | 3 | |
| β-strand | 119-120 | 2 | 12 |
| α-helix | 122-125 | 4 | |
| α-helix | 128-130 | 3 | |
| β-strand | 162-163 | 2 | 12 |
| β-strand | 168-180 | 13 | 9 |
| β-strand | 185-189 | 5 | 9 |
| β-strand | 199-204 | 6 | 9 |
Chain E: 9 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| β-strand | 7 | 1 | 13 |
| α-helix | 9-11 | 3 | |
| α-helix | 21-24 | 4 | |
| α-helix | 30-42 | 13 | |
| α-helix | 103-119 | 17 | |
| β-strand | 123-126 | 4 | 13 |
| α-helix | 136-145 | 10 | |
| β-strand | 152-156 | 5 | 13 |
| α-helix | 161-166 | 6 | |
| β-strand | 175-177 | 3 | 13 |
| α-helix | 183-188 | 6 | |
| β-strand | 191-195 | 5 | 13 |
| α-helix | 196-205 | 10 | |
Chain F: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 25-27 | 3 | 14 |
| β-strand | 34-36 | 3 | 14 |
| β-strand | 44-47 | 4 | 15 |
| β-strand | 50-53 | 4 | 15 |
| α-helix | 60-81 | 22 | |
Chain G: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-11 | 3 | |
| β-strand | 16-20 | 5 | 16 |
| β-strand | 25 | 1 | 17 |
| α-helix | 26-38 | 13 | |
| β-strand | 54-58 | 5 | 16 |
| β-strand | 64 | 1 | 17 |
| α-helix | 69-71 | 3 | |
| β-strand | 74-76 | 3 | 18 |
| β-strand | 87-89 | 3 | 18 |
| α-helix | 90-95 | 6 | |
| α-helix | 100-108 | 9 | |
| α-helix | 114-119 | 6 | |
| α-helix | 120-122 | 3 | |
| β-strand | 123-125 | 3 | 16 |
| β-strand | 139-140 | 2 | 16 |
Chain H: 2 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-10 | 4 | 19 |
| β-strand | 16-24 | 9 | 19 |
| β-strand | 38-46 | 9 | 19 |
| β-strand | 57-64 | 8 | 19 |
| β-strand | 68 | 1 | 20 |
| β-strand | 78 | 1 | 20 |
| β-strand | 83-86 | 4 | 19 |
| β-strand | 87 | 1 | 21 |
| β-strand | 93 | 1 | 21 |
| β-strand | 101-102 | 2 | 22 |
| α-helix | 104-107 | 4 | |
| α-helix | 112-117 | 6 | |
| β-strand | 120-121 | 2 | 22 |
Chain I: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-9 | 2 | |
| α-helix | 73-74 | 2 | |
| β-strand | 75-77 | 3 | 23 |
| α-helix | 79-82 | 4 | |
| α-helix | 93-99 | 7 | |
| β-strand | 109-111 | 3 | 23 |
| β-strand | 123-125 | 3 | 24 |
| β-strand | 127 | 1 | 23 |
| α-helix | 133-136 | 4 | |
| β-strand | 143-145 | 3 | 24 |
Chain J: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-27 | 18 | |
| β-strand | 29-33 | 5 | 25 |
| α-helix | 34-50 | 17 | |
| α-helix | 56-63 | 8 | |
| α-helix | 79-82 | 4 | |
| α-helix | 83-87 | 5 | |
| α-helix | 88-90 | 3 | |
| β-strand | 99-106 | 8 | 25 |
| β-strand | 113-119 | 7 | 25 |
15 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 |
|---|
| 23S rRNA | A | RNA | 2927 | Bacillus subtilis subsp. subtilis str. 168 | |
| 5S rRNA | B | RNA | 119 | Bacillus subtilis subsp. subtilis str. 168 | |
| Large ribosomal subunit protein uL2 | C | protein | 277 | Bacillus subtilis subsp. subtilis str. 168 | P42919 (AlphaFold model) |
| Large ribosomal subunit protein uL3 | D | protein | 209 | Bacillus subtilis subsp. subtilis str. 168 | P42920 (AlphaFold model) |
| Large ribosomal subunit protein uL4 | E | protein | 207 | Bacillus subtilis subsp. subtilis str. 168 | P42921 (AlphaFold model) |
| Large ribosomal subunit protein uL6 | F | protein | 179 | Bacillus subtilis subsp. subtilis str. 168 | P46898 (AlphaFold model) |
| Large ribosomal subunit protein uL13 | G | protein | 145 | Bacillus subtilis subsp. subtilis str. 168 | P70974 |
| Large ribosomal subunit protein uL14 | H | protein | 122 | Bacillus subtilis subsp. subtilis str. 168 | P12875 |
| Large ribosomal subunit protein uL15 | I | protein | 146 | Bacillus subtilis subsp. subtilis str. 168 | P19946 |
| Large ribosomal subunit protein bL17 | J | protein | 120 | Bacillus subtilis subsp. subtilis str. 168 | P20277 |
| Large ribosomal subunit protein bL19 | K | protein | 115 | Bacillus subtilis subsp. subtilis str. 168 | O31742 |
| Large ribosomal subunit protein bL20 | L | protein | 118 | Bacillus subtilis subsp. subtilis str. 168 | P55873 |
13 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>9BS0_1 23S rRNA (chains A)
GGUUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAUGAAGGACGGG
ACGAACACCGAUAUGCUUCGGGGAGCUGUAAGCAAGCUUUGAUCCGGAGAUUUCCGAAUG
GGGAAACCCACCACUCGUAAUGGAGUGGUAUCCAUAUCUGAAUUCAUAGGAUAUGAGAAG
GCAGACCCGGGGAACUGAAACAUCUAAGUACCCGGAGGAAGAGAAAGCAAAUGCGAUUCC
CUGAGUAGCGGCGAGCGAAACGGGAUCAGCCCAAACCAAGAGGCUUGCCUCUUGGGGUUG
UAGGACACUCUGUACGGAGUUACAAAGGAACGAGGUAGAUGAAGAGGUCUGGAAAGGCCC
GCCAUAGGAGGUAACAGCCCUGUAGUCAAAACUUCGUUCUCUCCUGAGUGGAUCCUGAGU
ACGGCGGAACACGUGAAAUUCCGUCGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAUAC
UCCCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGG
GGAGUGAAAGAGAUCCUGAAACCGUGUGCCUACAAGUAGUCAGAGCCCGUUAACGGGUGA
UGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUCUCGUGCAAGGUUAAGCAGAAG
AUGCGGAGCCGCAGCGAAAGCGAGUCUGAAUAGGGCGCAUGAGUACGUGGUCGUAGACCC
GAAACCAGGUGAUCUACCCAUGUCCAGGGUGAAGUUCAGGUAACACUGAAUGGAGGCCCG
AACCCACGCACGUUGAAAAGUGCGGGGAUGAGGUGUGGGUAGGGGUGAAAUGCCAAUCGA
ACCUGGAGAUAGCUGGUUCUCUCCGAAAUAGCUUUAGGGCUAGCCUCAAGGUAAGAGUCU
UGGAGGUAGAGCACUGAUUGGACUAGGGGCCCCUACCGGGUUACCGAAUUCAGUCAAACU
CCGAAUGCCAAUGACUUAUCCUUGGGAGUCAGACUGCGAGUGAUAAGAUCCGUAGUCGAA
AGGGAAACAGCCCAGACCGCCAGCUAAGGUCCCAAAGUAUACGUUAAGUGGAAAAGGAUG
UGGAGUUGCUUAGACAACCAGGAUGUUGGCUUAGAAGCAGCCACCAUUUAAAGAGUGCGU
AAUAGCUCACUGGUCGAGUGACUCUGCGCCGAAAAUGUACCGGGGCUAAACGUAUCACCG
AAGCUGCGGACUGUUCUUCGAACAGUGGUAGGAGAGCGUUCUAAGGGCUGUGAAGCCAGA
CCGGAAGGACUGGUGGAGCGCUUAGAAGUGAGAAUGCCGGUAUGAGUAGCGAAAGAGGGG
UGAGAAUCCCCUCCACCGAAUGCCUAAGGUUUCCUGAGGAAGGCUCGUCCGCUCAGGGUU
AGUCGGGACCUAAGCCGAGGCCGAAAGGCGUAGGCGAUGGACAACAGGUUGAUAUUCCUG
UACCACCUCCUCACCAUUUGAGCAAUGGGGGGACGCAGGAGGAUAGGGUAAGCGCGGUAU
UGGAUAUCCGCGUCCAAGCAGUUAGGCUGGGAAAUAGGCAAAUCCGUUUCCCAUAAGCCU
GAGCUGUGAUGGCGAGCGAAAUAUAGUAGCGAAGUUCCUGAUUCCACACUGCCAAGAAAA
GCCUCUAGCGAGGUGAGAGGUGCCCGUACCGCAAACCGACACAGGUAGGCGAGGAGAGAA
UCCUAAGGUGAUCGAGAGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCG
GGAGAAGGGGUGCUCUGUUAGGGUGCAAGCCCGAGAGAGCCGCAGUGAAUAGGCCCAGGC
GACUGUUUAGCAAAAACACAGGUCUCUGCGAAGCCGUAAGGCGAAGUAUAGGGGCUGACG
CCUGCCCGGUGCUGGAAGGUUAAGAGGAGCGCUUAGCGUAAGCGAAGGUGCGAAUUGAAG
CCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGU
AAGUUCCGACCCGCACGAAAGGCGCAACGAUCUGGGCACUGUCUCAACGAGAGACUCGGU
GAAAUUAUAGUACCUGUGAAGAUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGA
GCUUUACUGCAGCCUGAUAUUGAAUGUUGGUACAGCUUGUACAGGAUAGGUAGGAGCCUU
GGAAACCGGAGCGCCAGCUUCGGUGGAGGCAUCGGUGGGAUACUACCCUGGCUGUAUUGA
CCUUCUAACCCGCCGCCCUUAUCGGGCGGGGAGACAGUGUCAGGUGGGCAGUUUGACUGG
GGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUUCCCUCAGAAUGGUUGGAAA
UCAUUCGCAGAGUGUAAAGGCACAAGGGAGCUUGACUGCGAGACCUACAAGUCGAGCAGG
GACGAAAGUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACGGAU
AAAAGCUACCCCGGGGAUAACAGGCUUAUCUCCCCCAAGAGUCCACAUCGACGGGGAGGU
UUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGC
UGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCC
CUAUCCGUCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGA
UGGACGCACCGCUGGUGUACCAGUUGUUCUGCCAAGGGCAUCGCUGGGUAGCUAUGUGCG
GACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAU
UCCGCAAGGAAGUAAGAUCCCUGAAAGAUGAUCAGGUUGAUAGGUCUGAGGUGGAAGUGU
GGCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAACCA
Sequence of entity 2 (B), FASTA
>9BS0_2 5S rRNA (chains B)
UUUGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUC
UUCAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAAGCAAG
Sequence of entity 3 (C), FASTA
>9BS0_3 Large ribosomal subunit protein uL2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK
Sequence of entity 4 (D), FASTA
>9BS0_4 Large ribosomal subunit protein uL3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK
Sequence of entity 5 (E), FASTA
>9BS0_5 Large ribosomal subunit protein uL4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA
Sequence of entity 6 (F), FASTA
>9BS0_6 Large ribosomal subunit protein uL6 (chains F)
MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQK
EHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEE
GIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK
Sequence of entity 7 (G), FASTA
>9BS0_7 Large ribosomal subunit protein uL13 (chains G)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG
Sequence of entity 8 (H), FASTA
>9BS0_8 Large ribosomal subunit protein uL14 (chains H)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI
Sequence of entity 9 (I), FASTA
>9BS0_9 Large ribosomal subunit protein uL15 (chains I)
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQR
LPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKK
LTVKANKFSASAKEAVEAAGGTAEVI
Sequence of entity 10 (J), FASTA
>9BS0_10 Large ribosomal subunit protein bL17 (chains J)
MSYRKLGRTSAQRKAMLRDLTTDLIINERIETTETRAKELRSVVEKMITLGKRGDLHARR
QAAAYIRNEVANEENNQDALQKLFSDIATRYEERQGGYTRIMKLGPRRGDGAPMAIIELV
Sequence of entity 11 (K), FASTA
>9BS0_11 Large ribosomal subunit protein bL19 (chains K)
MQKLIEDITKEQLRTDLPAFRPGDTLRVHVKVVEGNRERIQIFEGVVIKRRGGGISETFT
VRKISYGVGVERTFPVHTPKIAKIEVVRYGKVRRAKLYYLRELRGKAARIKEIRR
Sequence of entity 12 (L), FASTA
>9BS0_12 Large ribosomal subunit protein bL20 (chains L)
PRVKGGTVTRKRRKKVLKLAKGYFGSKHTLYKVANQQVMKSGNYAFRDRRQKKRDFRKLW
ITRINAAARMNGLSYSRLMHGLKLSGIEVNRKMLADLAVNDLTAFNQLADAAKAQLNK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GNP | Phosphoaminophosphonic acid-guanylate ester | C10 H17 N6 O13 P3 | 2 |
Primary citation
The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly. Arpin, D., Palacios, A., Basu, K. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkae1197 · PubMed
Other PDB entries of the same protein (UniProt P42919 (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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