6PPF: Bacterial 45SRbgA ribosomal particle class B
Bacterial 45SRbgA ribosomal particle class B. Determined by electron microscopy at 3.4 Å resolution. Released 18 Sept 2019.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organism
- Bacillus subtilis
- Chains
- 21
- Atoms
- 71,835
- Mol. weight
- 1244.56 kDa
- Released
- 18 Sept 2019
Explore 6PPF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6PPF contains 81 α-helices and 140 β-strands across 19 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 b: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-14 | 4 | |
| α-helix | 24-26 | 3 | |
| β-strand | 27-29 | 3 | 50 |
| β-strand | 36-38 | 3 | 50 |
Chain C: 8 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 1 |
| α-helix | 6-7 | 2 | |
| 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 | 1 | |
| β-strand | 76-81 | 6 | 4 |
| α-helix | 90 | 1 | |
| 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 | 135-136 | 2 | |
| β-strand | 140 | 1 | 7 |
| β-strand | 141-142 | 2 | 6 |
| β-strand | 145 | 1 | 8 |
| β-strand | 152 | 1 | 8 |
| β-strand | 163-167 | 5 | 7 |
| β-strand | 171-175 | 5 | 7 |
| α-helix | 177-179 | 3 | |
| β-strand | 181-185 | 5 | 7 |
| β-strand | 189-192 | 4 | 6 |
| β-strand | 195 | 1 | 5 |
| α-helix | 198-200 | 3 | |
| α-helix | 210-213 | 4 | |
Chain d: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 25-37 | 13 | |
Chain D: 4 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-8 | 4 | 9 |
| β-strand | 11-12 | 2 | 10 |
| β-strand | 15-16 | 2 | 11 |
| β-strand | 22-23 | 2 | 11 |
| β-strand | 25-29 | 5 | 10 |
| β-strand | 37-39 | 3 | 12 |
| β-strand | 48-55 | 8 | 12 |
| α-helix | 63-65 | 3 | |
| α-helix | 70-72 | 3 | |
| α-helix | 75-76 | 2 | |
| β-strand | 77-82 | 6 | 12 |
| α-helix | 99-101 | 3 | |
| β-strand | 108-110 | 3 | 9 |
| β-strand | 113 | 1 | 13 |
| β-strand | 119-120 | 2 | 14 |
| β-strand | 162-163 | 2 | 14 |
| β-strand | 168 | 1 | 13 |
| β-strand | 171-174 | 4 | 9 |
| β-strand | 176-179 | 4 | 10 |
| β-strand | 185-189 | 5 | 10 |
| β-strand | 199-204 | 6 | 9 |
Chain E: 10 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-5 | 2 | |
| β-strand | 6-7 | 2 | 15 |
| α-helix | 21-24 | 4 | |
| α-helix | 26-28 | 3 | |
| α-helix | 35-41 | 7 | |
| α-helix | 103-119 | 17 | |
| β-strand | 123-126 | 4 | 15 |
| α-helix | 137-146 | 10 | |
| β-strand | 154-156 | 3 | 15 |
| α-helix | 161-166 | 6 | |
| β-strand | 175-177 | 3 | 15 |
| α-helix | 178-180 | 3 | |
| α-helix | 183-189 | 7 | |
| β-strand | 192-195 | 4 | 15 |
| α-helix | 196-205 | 10 | |
Chain J: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-19 | 4 | 16 |
| α-helix | 26-30 | 5 | |
| α-helix | 33-37 | 5 | |
| β-strand | 54-57 | 4 | 16 |
| α-helix | 69-71 | 3 | |
| β-strand | 75-76 | 2 | 17 |
| β-strand | 87-88 | 2 | 17 |
| α-helix | 90-93 | 4 | |
| α-helix | 98-109 | 12 | |
| α-helix | 115-118 | 4 | |
| α-helix | 120-122 | 3 | |
| β-strand | 123-125 | 3 | 16 |
| α-helix | 134-136 | 3 | |
| β-strand | 139-140 | 2 | 16 |
Chain K: 2 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-10 | 3 | 18 |
| β-strand | 12 | 1 | 19 |
| β-strand | 16 | 1 | 20 |
| β-strand | 18-24 | 7 | 18 |
| β-strand | 38-43 | 6 | 18 |
| β-strand | 46 | 1 | 20 |
| β-strand | 57-62 | 6 | 18 |
| β-strand | 69-70 | 2 | 21 |
| β-strand | 76-77 | 2 | 21 |
| β-strand | 83-87 | 5 | 18 |
| β-strand | 98 | 1 | 19 |
| β-strand | 102 | 1 | 22 |
| α-helix | 104-107 | 4 | |
| α-helix | 112-115 | 4 | |
| β-strand | 121 | 1 | 22 |
Chain L: 7 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| α-helix | 23-25 | 3 | |
| α-helix | 57-59 | 3 | |
| α-helix | 62-63 | 2 | |
| β-strand | 75-77 | 3 | 23 |
| α-helix | 79-81 | 3 | |
| β-strand | 91 | 1 | 24 |
| α-helix | 93-99 | 7 | |
| β-strand | 109-111 | 3 | 23 |
| β-strand | 123-124 | 2 | 24 |
| β-strand | 127-128 | 2 | 23 |
| α-helix | 130-139 | 10 | |
| β-strand | 143-144 | 2 | 24 |
11 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 | |
| 5S rRNA | B | RNA | 119 | Bacillus subtilis | |
| 50S ribosomal protein L2 | C | protein | 277 | Bacillus subtilis | P42919 (AlphaFold model) |
| 50S ribosomal protein L3 | D | protein | 209 | Bacillus subtilis | P42920 (AlphaFold model) |
| 50S ribosomal protein L4 | E | protein | 207 | Bacillus subtilis | P42921 (AlphaFold model) |
| 50S ribosomal protein L13 | J | protein | 145 | Bacillus subtilis | P70974 (AlphaFold model) |
| 50S ribosomal protein L14 | K | protein | 122 | Bacillus subtilis | P12875 |
| 50S ribosomal protein L15 | L | protein | 145 | Bacillus subtilis | P19946 |
| 50S ribosomal protein L17 | N | protein | 120 | Bacillus subtilis | P20277 |
| 50S ribosomal protein L18 | O | protein | 120 | Bacillus subtilis | P46899 |
| 50S ribosomal protein L19 | P | protein | 115 | Bacillus subtilis | O31742 |
| 50S ribosomal protein L20 | Q | protein | 118 | Bacillus subtilis | P55873 |
9 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6PPF_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
UGGAUAUCCGCGUCCAAGCAGUUAGGCUGGGAAAUAGGCAAAUCCGUUUCCCAUAAGGCU
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
>6PPF_2 5S rRNA (chains B)
UUUGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUC
UUCAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAAGCAAG
Sequence of entity 3 (C), FASTA
>6PPF_3 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK
Sequence of entity 4 (D), FASTA
>6PPF_4 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK
Sequence of entity 5 (E), FASTA
>6PPF_5 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA
Sequence of entity 6 (J), FASTA
>6PPF_6 50S ribosomal protein L13 (chains J)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG
Sequence of entity 7 (K), FASTA
>6PPF_7 50S ribosomal protein L14 (chains K)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI
Sequence of entity 8 (L), FASTA
>6PPF_8 50S ribosomal protein L15 (chains L)
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQR
LPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKK
LTVKANKFSASAKEAVEAAGGTAEV
Sequence of entity 9 (N), FASTA
>6PPF_9 50S ribosomal protein L17 (chains N)
MSYRKLGRTSAQRKAMLRDLTTDLIINERIETTETRAKELRSVVEKMITLGKRGDLHARR
QAAAYIRNEVANEENNQDALQKLFSDIATRYEERQGGYTRIMKLGPRRGDGAPMAIIELV
Sequence of entity 10 (O), FASTA
>6PPF_10 50S ribosomal protein L18 (chains O)
MITKTSKNAARLKRHARVRAKLSGTAERPRLNVFRSNKHIYAQIIDDVNGVTLASASTLD
KDLNVESTGDTSAATKVGELVAKRAAEKGISDVVFDRGGYLYHGRVKALADAAREAGLKF
Sequence of entity 11 (P), FASTA
>6PPF_11 50S ribosomal protein L19 (chains P)
MQKLIEDITKEQLRTDLPAFRPGDTLRVHVKVVEGNRERIQIFEGVVIKRRGGGISETFT
VRKISYGVGVERTFPVHTPKIAKIEVVRYGKVRRAKLYYLRELRGKAARIKEIRR
Sequence of entity 12 (Q), FASTA
>6PPF_12 50S ribosomal protein L20 (chains Q)
PRVKGGTVTRKRRKKVLKLAKGYFGSKHTLYKVANQQVMKSGNYAFRDRRQKKRDFRKLW
ITRINAAARMNGLSYSRLMHGLKLSGIEVNRKMLADLAVNDLTAFNQLADAAKAQLNK
Primary citation
Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate. Seffouh, A., Jain, N., Jahagirdar, D. et al. Nucleic Acids Res (2019) 47:10414-10425. DOI 10.1093/nar/gkz770 · 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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