3J3V: 50S ribosomal protein L32
Atomic model of the immature 50S subunit from Bacillus subtilis (state I-a). Determined by electron microscopy at 13.3 Å resolution. Released 12 Jun 2013.
- Method
- Electron microscopy
- Resolution
- 13.3 Å
- Organism
- Bacillus subtilis
- Chains
- 24
- Atoms
- 86,157
- Mol. weight
- 1314.1 kDa
- Released
- 12 Jun 2013
Explore 3J3V in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3J3V contains 78 α-helices and 117 β-strands across 22 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: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-16 | 7 | |
| β-strand | 28-30 | 3 | 1 |
| β-strand | 35-37 | 3 | 1 |
Chain 2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-15 | 7 | |
| α-helix | 18-21 | 4 | |
| α-helix | 25-37 | 13 | |
Chain 5: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-15 | 10 | |
| α-helix | 23-29 | 7 | |
| β-strand | 43-44 | 2 | 2 |
| α-helix | 55-57 | 3 | |
| α-helix | 182-198 | 17 | |
| β-strand | 213-215 | 3 | 2 |
| β-strand | 221-223 | 3 | 2 |
Chain 6: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-14 | 6 | 3 |
| α-helix | 22-24 | 3 | |
| α-helix | 35-46 | 12 | |
| β-strand | 53-59 | 7 | 3 |
| β-strand | 67-70 | 4 | 3 |
| α-helix | 71-74 | 4 | |
| α-helix | 75-83 | 9 | |
| α-helix | 102-111 | 10 | |
| α-helix | 113-115 | 3 | |
| α-helix | 121-135 | 15 | |
Chain C: 2 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 4 |
| β-strand | 17-19 | 3 | 4 |
| β-strand | 38-39 | 2 | 5 |
| β-strand | 60-61 | 2 | 5 |
| β-strand | 65-66 | 2 | 6 |
| β-strand | 76-82 | 7 | 6 |
| β-strand | 91-96 | 6 | 6 |
| β-strand | 101-105 | 5 | 6 |
| β-strand | 107 | 1 | 7 |
| β-strand | 115-116 | 2 | 6 |
| β-strand | 129-131 | 3 | 8 |
| α-helix | 140 | 1 | |
| β-strand | 141-142 | 2 | 8 |
| β-strand | 144 | 1 | 9 |
| β-strand | 154 | 1 | 9 |
| β-strand | 163-168 | 6 | 10 |
| β-strand | 171-175 | 5 | 10 |
| β-strand | 181-185 | 5 | 10 |
| β-strand | 189-192 | 4 | 8 |
| β-strand | 195 | 1 | 7 |
| α-helix | 218-221 | 4 | |
Chain D: 2 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 11 |
| β-strand | 13-15 | 3 | 11 |
| β-strand | 23-30 | 8 | 11 |
| β-strand | 33-34 | 2 | 12 |
| β-strand | 35-39 | 5 | 13 |
| β-strand | 48-52 | 5 | 13 |
| β-strand | 55 | 1 | 14 |
| α-helix | 63-70 | 8 | |
| β-strand | 77 | 1 | 14 |
| β-strand | 80-84 | 5 | 13 |
| β-strand | 95-96 | 2 | 12 |
| β-strand | 107-113 | 7 | 11 |
| β-strand | 116-120 | 5 | 15 |
| α-helix | 154-156 | 3 | |
| β-strand | 162-165 | 4 | 15 |
| β-strand | 168-180 | 13 | 11 |
| β-strand | 185-189 | 5 | 11 |
| β-strand | 199-204 | 6 | 11 |
Chain E: 6 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-4 | 2 | 16 |
| β-strand | 17-18 | 2 | 16 |
| α-helix | 30-35 | 6 | |
| α-helix | 38-41 | 4 | |
| β-strand | 84 | 1 | 17 |
| β-strand | 86 | 1 | 17 |
| α-helix | 103-119 | 17 | |
| β-strand | 125 | 1 | 18 |
| α-helix | 136-145 | 10 | |
| α-helix | 184-187 | 4 | |
| β-strand | 194 | 1 | 18 |
| α-helix | 196-206 | 11 | |
Chain F: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-7 | 5 | |
| α-helix | 8-12 | 5 | |
| α-helix | 13-19 | 7 | |
| α-helix | 24-27 | 4 | |
| β-strand | 31-37 | 7 | 19 |
| α-helix | 52-61 | 10 | |
| β-strand | 90 | 1 | 19 |
| α-helix | 94-105 | 12 | |
| β-strand | 122 | 1 | 19 |
| β-strand | 128-131 | 4 | 19 |
| β-strand | 153-158 | 6 | 19 |
14 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 |
|---|
| 50S ribosomal protein L32 | 0 | protein | 59 | Bacillus subtilis | O34687 (AlphaFold model) |
| 50S ribosomal protein L34 | 2 | protein | 44 | Bacillus subtilis | P05647 (AlphaFold model) |
| 50S ribosomal protein L1 | 5 | protein | 232 | Bacillus subtilis | Q06797 (AlphaFold model) |
| 50S ribosomal protein L11 | 6 | protein | 141 | Bacillus subtilis | Q06796 (AlphaFold model) |
| ribosome RNA 23S | A | RNA | 2927 | Bacillus subtilis | |
| ribosome RNA 5S | B | RNA | 119 | Bacillus subtilis | |
| 50S ribosomal protein L2 | C | protein | 277 | Bacillus subtilis | P42919 |
| 50S ribosomal protein L3 | D | protein | 209 | Bacillus subtilis | P42920 |
| 50S ribosomal protein L4 | E | protein | 207 | Bacillus subtilis | P42921 |
| 50S ribosomal protein L5 | F | protein | 179 | Bacillus subtilis | P12877 |
| 50S ribosomal protein L6 | G | protein | 179 | Bacillus subtilis | P46898 |
| 50S ribosomal protein L13 | J | protein | 145 | Bacillus subtilis | P70974 |
12 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>3J3V_1 50S ribosomal protein L32 (chains 0)
MAVPFRRTSKMKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNGKDINVKSN
Sequence of entity 2 (2), FASTA
>3J3V_2 50S ribosomal protein L34 (chains 2)
MKRTFQPNNRKRSKVHGFRSRMSSKNGRLVLARRRRKGRKVLSA
Sequence of entity 3 (5), FASTA
>3J3V_3 50S ribosomal protein L1 (chains 5)
MAKKGKKYVEAAKLVDRSKAYDVSEAVALVKKTNTAKFDATVEVAFRLGVDPRKNDQQIR
GAVVLPNGTGKTQRVLVFAKGEKAKEAEAAGADFVGDTDYINKIQQGWFDFDVIVATPDM
MGEVGKIGRVLGPKGLMPNPKTGTVTFEVEKAIGEIKAGKVEYRVDKAGNIHVPIGKVSF
EDEKLVENFTTMYDTILKAKPAAAKGVYVKNVAVTSTMGPGVKVDSSTFNVK
Sequence of entity 4 (6), FASTA
>3J3V_4 50S ribosomal protein L11 (chains 6)
MAKKVVKVVKLQIPAGKANPAPPVGPALGQAGVNIMGFCKEFNARTADQAGLIIPVEISV
YEDRSFTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATVKRDKVREIAETKMPDLNAAD
VEAAMRMVEGTARSMGIVIED
Sequence of entity 5 (A), FASTA
>3J3V_5 ribosome RNA 23S (chains A)
GGUUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAUGAAGGACGGG
ACGAACACCGAUAUGCUUCGGGGAGCUGUAAGCAAGCUUUGAUCCGGAGAUUUCCGAAUG
GGGAAACCCACCACUCGUAAUGGAGUGGUAUCCAUAUCUGAAUUCAUAGGAUAUGAGAAG
GCAGACCCGGGGAACUGAAACAUCUAAGUACCCGGAGGAAGAGAAAGCAAAUGCGAUUCC
CUGAGUAGCGGCGAGCGAAACGGGAUUAGCCCAAACCAAGAGGCUUGCCUCUUGGGGUUG
UAGGACACUCUGUACGGAGUUACAAAGGAACGAGGUAGAUGAAGAGGUCUGGAAAGGCCC
GCCAUAGGAGGUAACAGCCCUGUAGUCAAAACUUCGUUCUCUCCUGAGUGGAUCCUGAGU
ACGGCGGAACACGUGAAAUUCCGUCGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAUAC
UCCCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGG
GGAGUGAAAGAGAUCCUGAAACCGUGUGCCUACAAGUAGUCAGAGCCCGUUAACGGGUGA
UGGCGUGCCUUUUGUAGAAUGAACCGGCGAGUUACGAUCCCGUGCAAGGUUAAGCAGAAG
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
UUGGCACCUCGAUGUCGGCUCAUCGCAUCCUGGGGCUGUAGUCAGUCCCAAGGGUUGGGC
UGUUCGCCCAUUAAAGCGGUACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCC
CUAUCCGUCGCGGGCGCAGGAAAUUUGAGAGGAGCUGUCCUUAGUACGAGAGGACCGGGA
UGGACGCACCGCUGGUGUACCAGUUGUUCUGCCAAGGGCAUCGCUGGGUAGCUAUGUGCG
GACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAU
UCCGCAAGGAAGUAAGAUCCCUGAAAGAUGAUCAGGUUGAUAGGUCUGAGGUGGAAGUGU
GGCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAACCA
Sequence of entity 6 (B), FASTA
>3J3V_6 ribosome RNA 5S (chains B)
UUUGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUC
UUCAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAAGCAAG
Sequence of entity 7 (C), FASTA
>3J3V_7 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK
Sequence of entity 8 (D), FASTA
>3J3V_8 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK
Sequence of entity 9 (E), FASTA
>3J3V_9 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA
Sequence of entity 10 (F), FASTA
>3J3V_10 50S ribosomal protein L5 (chains F)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK
Sequence of entity 11 (G), FASTA
>3J3V_11 50S ribosomal protein L6 (chains G)
MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQK
EHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEE
GIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK
Sequence of entity 12 (J), FASTA
>3J3V_12 50S ribosomal protein L13 (chains J)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG
Primary citation
Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit. Li, N., Chen, Y., Guo, Q. et al. Nucleic Acids Res (2013) 41:7073-7083. DOI 10.1093/nar/gkt423 · 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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