3J3W: 50S ribosomal protein L32
Atomic model of the immature 50S subunit from Bacillus subtilis (state II-a). Determined by electron microscopy at 10.7 Å resolution. Released 12 Jun 2013.
- Method
- Electron microscopy
- Resolution
- 10.7 Å
- Organism
- Bacillus subtilis
- Chains
- 20
- Atoms
- 76,573
- Mol. weight
- 1235.85 kDa
- Released
- 12 Jun 2013
Explore 3J3W in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3J3W contains 59 α-helices and 116 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 0: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-17 | 8 | |
| 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 | 18-23 | 6 | |
| α-helix | 25-37 | 13 | |
Chain 5: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-14 | 9 | |
| α-helix | 23-32 | 10 | |
| β-strand | 44 | 1 | 35 |
| α-helix | 55-57 | 3 | |
| α-helix | 182-198 | 17 | |
| β-strand | 213-216 | 4 | 35 |
| β-strand | 219-223 | 5 | 35 |
Chain 6: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-14 | 7 | 36 |
| β-strand | 53-59 | 7 | 36 |
| β-strand | 67-70 | 4 | 36 |
| α-helix | 71-72 | 2 | |
| α-helix | 74 | 1 | |
| α-helix | 75-83 | 9 | |
| β-strand | 99-100 | 2 | 37 |
| α-helix | 102-112 | 11 | |
| α-helix | 113-115 | 3 | |
| α-helix | 121-135 | 15 | |
| β-strand | 138-139 | 2 | 37 |
Chain C: 3 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16 | 1 | 2 |
| α-helix | 18-20 | 3 | |
| β-strand | 37-40 | 4 | 3 |
| β-strand | 59-62 | 4 | 3 |
| α-helix | 64 | 1 | |
| β-strand | 65-66 | 2 | 4 |
| β-strand | 76-83 | 8 | 4 |
| β-strand | 90-96 | 7 | 4 |
| β-strand | 101-105 | 5 | 4 |
| β-strand | 115-116 | 2 | 4 |
| β-strand | 118 | 1 | 5 |
| β-strand | 129-131 | 3 | 5 |
| β-strand | 141-142 | 2 | 5 |
| β-strand | 144 | 1 | 6 |
| β-strand | 154 | 1 | 6 |
| β-strand | 162-168 | 7 | 7 |
| β-strand | 171-176 | 6 | 7 |
| β-strand | 181-185 | 5 | 7 |
| β-strand | 189-192 | 4 | 5 |
| β-strand | 205 | 1 | 2 |
| α-helix | 211-213 | 3 | |
| β-strand | 270-271 | 2 | 7 |
Chain D: 2 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-17 | 14 | 21 |
| β-strand | 21-30 | 10 | 21 |
| β-strand | 33-34 | 2 | 22 |
| β-strand | 35-37 | 3 | 23 |
| β-strand | 49-52 | 4 | 23 |
| β-strand | 55 | 1 | 24 |
| α-helix | 63-70 | 8 | |
| β-strand | 77 | 1 | 24 |
| β-strand | 80-83 | 4 | 23 |
| β-strand | 95-96 | 2 | 22 |
| β-strand | 99 | 1 | 25 |
| β-strand | 102 | 1 | 25 |
| β-strand | 107-113 | 7 | 21 |
| α-helix | 114-115 | 2 | |
| β-strand | 116-120 | 5 | 26 |
| β-strand | 162-165 | 4 | 26 |
| β-strand | 168-179 | 12 | 21 |
| β-strand | 185-189 | 5 | 21 |
| β-strand | 198-204 | 7 | 21 |
Chain E: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 38 |
| β-strand | 16-18 | 3 | 38 |
| α-helix | 30-41 | 12 | |
| α-helix | 105-119 | 15 | |
| β-strand | 125-126 | 2 | 39 |
| α-helix | 136-146 | 11 | |
| β-strand | 152 | 1 | 40 |
| β-strand | 155 | 1 | 39 |
| β-strand | 173 | 1 | 40 |
| β-strand | 176 | 1 | 39 |
| α-helix | 183-188 | 6 | |
| β-strand | 194-195 | 2 | 39 |
| α-helix | 196-201 | 6 | |
| α-helix | 202-204 | 3 | |
Chain G: 2 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-20 | 5 | 9 |
| β-strand | 24-29 | 6 | 9 |
| β-strand | 32-37 | 6 | 9 |
| β-strand | 43-47 | 5 | 10 |
| β-strand | 50-54 | 5 | 10 |
| α-helix | 60-82 | 23 | |
| β-strand | 85-91 | 7 | 11 |
| β-strand | 96-100 | 5 | 12 |
| β-strand | 103-107 | 5 | 12 |
| β-strand | 114-116 | 3 | 12 |
| β-strand | 122-128 | 7 | 11 |
| β-strand | 131-136 | 6 | 11 |
| α-helix | 139-151 | 13 | |
| β-strand | 162-164 | 3 | 11 |
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 |
|---|
| ribosome RNA 23S | A | RNA | 2927 | Bacillus subtilis | |
| 50S ribosomal protein L32 | 0 | protein | 59 | Bacillus subtilis | O34687 (AlphaFold model) |
| 50S ribosomal protein L2 | C | protein | 277 | Bacillus subtilis | P42919 (AlphaFold model) |
| 50S ribosomal protein L17 | N | protein | 120 | Bacillus subtilis | P20277 (AlphaFold model) |
| 50S ribosomal protein L6 | G | protein | 179 | Bacillus subtilis | P46898 (AlphaFold model) |
| 50S ribosomal protein L13 | J | protein | 145 | Bacillus subtilis | P70974 |
| 50S ribosomal protein L14 | K | protein | 122 | Bacillus subtilis | P12875 |
| 50S ribosomal protein L15 | L | protein | 146 | Bacillus subtilis | P19946 |
| 50S ribosomal protein L19 | P | protein | 115 | Bacillus subtilis | O31742 |
| 50S ribosomal protein L20 | Q | protein | 119 | Bacillus subtilis | P55873 |
| 50S ribosomal protein L3 | D | protein | 209 | Bacillus subtilis | P42920 |
| 50S ribosomal protein L21 | R | protein | 102 | Bacillus subtilis | P26908 |
8 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>3J3W_1 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 2 (0), FASTA
>3J3W_2 50S ribosomal protein L32 (chains 0)
MAVPFRRTSKMKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNGKDINVKSN
Sequence of entity 3 (C), FASTA
>3J3W_3 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK
Sequence of entity 4 (N), FASTA
>3J3W_4 50S ribosomal protein L17 (chains N)
MSYRKLGRTSAQRKAMLRDLTTDLIINERIETTETRAKELRSVVEKMITLGKRGDLHARR
QAAAYIRNEVANEENNQDALQKLFSDIATRYEERQGGYTRIMKLGPRRGDGAPMAIIELV
Sequence of entity 5 (G), FASTA
>3J3W_5 50S ribosomal protein L6 (chains G)
MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQK
EHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEE
GIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK
Sequence of entity 6 (J), FASTA
>3J3W_6 50S ribosomal protein L13 (chains J)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG
Sequence of entity 7 (K), FASTA
>3J3W_7 50S ribosomal protein L14 (chains K)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI
Sequence of entity 8 (L), FASTA
>3J3W_8 50S ribosomal protein L15 (chains L)
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQR
LPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKK
LTVKANKFSASAKEAVEAAGGTAEVI
Sequence of entity 9 (P), FASTA
>3J3W_9 50S ribosomal protein L19 (chains P)
MQKLIEDITKEQLRTDLPAFRPGDTLRVHVKVVEGNRERIQIFEGVVIKRRGGGISETFT
VRKISYGVGVERTFPVHTPKIAKIEVVRYGKVRRAKLYYLRELRGKAARIKEIRR
Sequence of entity 10 (Q), FASTA
>3J3W_10 50S ribosomal protein L20 (chains Q)
MPRVKGGTVTRKRRKKVLKLAKGYFGSKHTLYKVANQQVMKSGNYAFRDRRQKKRDFRKL
WITRINAAARMNGLSYSRLMHGLKLSGIEVNRKMLADLAVNDLTAFNQLADAAKAQLNK
Sequence of entity 11 (D), FASTA
>3J3W_11 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK
Sequence of entity 12 (R), FASTA
>3J3W_12 50S ribosomal protein L21 (chains R)
MYAIIKTGGKQIKVEEGQTVYIEKLAAEAGETVTFEDVLFVGGDNVKVGNPTVEGATVTA
KVEKQGRAKKITVFRYKPKKNVHKKQGHRQPYTKVTIEKINA
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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