6HA1: 50S ribosomal protein L2
Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycin. Determined by electron microscopy at 3.1 Å resolution. Released 29 Aug 2018.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organisms
- Bacillus subtilis (strain 168), Escherichia coli
- Chains
- 51
- Atoms
- 140,824
- Mol. weight
- 2137.09 kDa
- Ligands
- TEL
- Released
- 29 Aug 2018
Explore 6HA1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6HA1 contains 202 α-helices and 291 β-strands across 46 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: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-16 | 7 | |
| α-helix | 17-19 | 3 | |
| α-helix | 23-26 | 4 | |
| β-strand | 27-29 | 3 | 93 |
| β-strand | 36-38 | 3 | 93 |
| β-strand | 48-49 | 2 | 94 |
| β-strand | 52-53 | 2 | 94 |
Chain 1: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 95 |
| β-strand | 7-9 | 3 | 96 |
| β-strand | 18-22 | 5 | 95 |
| α-helix | 29-30 | 2 | |
| β-strand | 31-36 | 6 | 96 |
| β-strand | 41-47 | 7 | 96 |
Chain 2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-36 | 12 | |
Chain 3: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 8-13 | 6 | |
| β-strand | 15-16 | 2 | 1 |
| α-helix | 18-20 | 3 | |
| β-strand | 22-24 | 3 | 1 |
| α-helix | 38-44 | 7 | |
| β-strand | 48-49 | 2 | 1 |
| α-helix | 52-58 | 7 | |
| α-helix | 60-62 | 3 | |
Chain 4: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 2 |
| β-strand | 15-19 | 5 | 2 |
| β-strand | 22-26 | 5 | 2 |
| β-strand | 34-35 | 2 | 2 |
Chain 6: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-8 | 2 | |
| β-strand | 10-14 | 5 | 11 |
| β-strand | 22-26 | 5 | 11 |
| β-strand | 30-31 | 2 | 11 |
| α-helix | 49-53 | 5 | |
| α-helix | 55-57 | 3 | |
Chain b: 8 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17-18 | 2 | 19 |
| β-strand | 31-33 | 3 | 19 |
| β-strand | 39-41 | 3 | 19 |
| α-helix | 44-63 | 20 | |
| β-strand | 68-70 | 3 | 20 |
| α-helix | 74-87 | 14 | |
| β-strand | 90-92 | 3 | 20 |
| α-helix | 104-120 | 17 | |
| α-helix | 132 | 1 | |
| α-helix | 133-138 | 6 | |
| α-helix | 139-148 | 10 | |
| β-strand | 161-163 | 3 | 20 |
| α-helix | 170-179 | 10 | |
| β-strand | 183-187 | 5 | 20 |
| β-strand | 198-201 | 4 | 20 |
| α-helix | 207-222 | 16 | |
Chain c: 6 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| α-helix | 7-10 | 4 | |
| β-strand | 12 | 1 | 25 |
| β-strand | 16 | 1 | 25 |
| β-strand | 20 | 1 | 26 |
| α-helix | 28-45 | 18 | |
| β-strand | 53-56 | 4 | 26 |
| β-strand | 62-68 | 7 | 26 |
| α-helix | 80-94 | 15 | |
| β-strand | 97-103 | 7 | 26 |
| α-helix | 112-124 | 13 | |
| α-helix | 131-143 | 13 | |
| β-strand | 147-154 | 8 | 27 |
| β-strand | 163-170 | 8 | 27 |
| β-strand | 181-190 | 10 | 27 |
| β-strand | 193-202 | 10 | 27 |
38 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 ribosomal RNA | A | RNA | 2928 | Bacillus subtilis (strain 168) | |
| 5S ribosomal RNA | B | RNA | 112 | Bacillus subtilis (strain 168) | |
| 50S ribosomal protein L2 | C | protein | 277 | Bacillus subtilis (strain 168) | P42919 (AlphaFold model) |
| 50S ribosomal protein L3 | D | protein | 209 | Bacillus subtilis (strain 168) | P42920 (AlphaFold model) |
| 50S ribosomal protein L4 | E | protein | 207 | Bacillus subtilis (strain 168) | P42921 (AlphaFold model) |
| 50S ribosomal protein L5 | F | protein | 179 | Bacillus subtilis (strain 168) | P12877 (AlphaFold model) |
| 50S ribosomal protein L6 | G | protein | 179 | Bacillus subtilis (strain 168) | P46898 |
| 50S ribosomal protein L13 | J | protein | 145 | Bacillus subtilis (strain 168) | P70974 |
| 50S ribosomal protein L14 | K | protein | 122 | Bacillus subtilis (strain 168) | P12875 |
| 50S ribosomal protein L15 | L | protein | 146 | Bacillus subtilis (strain 168) | P19946 |
| 50S ribosomal protein L16 | M | protein | 144 | Bacillus subtilis (strain 168) | P14577 |
| 50S ribosomal protein L17 | N | protein | 120 | Bacillus subtilis (strain 168) | P20277 |
39 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6HA1_1 23S ribosomal RNA (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
GGCGACACAUGGAGCUGACAGAUACUAAUCGAUCGAGGACUUAACCAU
Sequence of entity 2 (B), FASTA
>6HA1_2 5S ribosomal RNA (chains B)
UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUU
CAGCGCCGAUGGUAGUCGGGGGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA
Sequence of entity 3 (C), FASTA
>6HA1_3 50S ribosomal protein L2 (chains C)
MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKR
QYRVIDFKRDKDGIPGRVATVEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGP
EADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGTSAQVLGKEGKYVLVRLNSGE
VRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP
IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK
Sequence of entity 4 (D), FASTA
>6HA1_4 50S ribosomal protein L3 (chains D)
MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKL
SNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQ
GAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLLPGRMGGEQITVQNLEIVKVD
AERNLLLIKGNVPGAKKSLITVKSAVKSK
Sequence of entity 5 (E), FASTA
>6HA1_5 50S ribosomal protein L4 (chains E)
MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGG
GRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVID
NNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADANEAVALSARNIPGVTVVEANG
INVLDVVNHEKLLITKAAVEKVEEVLA
Sequence of entity 6 (F), FASTA
>6HA1_6 50S ribosomal protein L5 (chains F)
MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFI
AGQKPVVTRAKKSIAGFRLREGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKK
SFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTANTDEEARELLTQVGMPFQK
Sequence of entity 7 (G), FASTA
>6HA1_7 50S ribosomal protein L6 (chains G)
MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQK
EHRALHGTTRSLLGNMVEGVSKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEE
GIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKGKGIRYEGEVVRRKEGKSAK
Sequence of entity 8 (J), FASTA
>6HA1_8 50S ribosomal protein L13 (chains J)
MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINA
EKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMF
KKLNVYRGSEHPHEAQKPEVYELRG
Sequence of entity 9 (K), FASTA
>6HA1_9 50S ribosomal protein L14 (chains K)
MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKA
VIVRTKSGARRSDGSYISFDENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPE
VI
Sequence of entity 10 (L), FASTA
>6HA1_10 50S ribosomal protein L15 (chains L)
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQR
LPKRGFTNINRKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKK
LTVKANKFSASAKEAVEAAGGTAEVI
Sequence of entity 11 (M), FASTA
>6HA1_11 50S ribosomal protein L16 (chains M)
MLLPKRVKYRREHRGKMRGRAKGGTEVHFGEFGIQALEASWITNRQIEAARIAMTRYMKR
GGKVWIKIFPSKPYTAKPLEVRMGSGKGAPEGWVAVVKPGKVLFEISGVSEEVAREALRL
ASHKLPIKTKFVKREEIGGESNES
Sequence of entity 12 (N), FASTA
>6HA1_12 50S ribosomal protein L17 (chains N)
MSYRKLGRTSAQRKAMLRDLTTDLIINERIETTETRAKELRSVVEKMITLGKRGDLHARR
QAAAYIRNEVANEENNQDALQKLFSDIATRYEERQGGYTRIMKLGPRRGDGAPMAIIELV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| TEL | Telithromycin | C43 H65 N5 O10 | 1 |
Primary citation
Structural basis for antibiotic resistance mediated by theBacillus subtilisABCF ATPase VmlR. Crowe-McAuliffe, C., Graf, M., Huter, P. et al. Proc Natl Acad Sci U S A (2018) 115:8978-8983. DOI 10.1073/pnas.1808535115 · 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
- 7AQD 3.1 Å, Structure of the bacterial RQC complex (Translocating State)
Browse structure collections
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