6BOH: 50S ribosomal protein L2

Antibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome. Determined by X-ray diffraction at 3.4 Å resolution. Released 23 May 2018.

Method
X-ray diffraction
Resolution
3.4 Å
Organisms
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039), Escherichia coli K-12, synthetic construct
Chains
114
Atoms
298,186
Mol. weight
4622.55 kDa
Ligands
ZN, BLS, MG
Released
23 May 2018

Explore 6BOH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BOH contains 476 α-helices and 685 β-strands across 102 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 AA: 2 helices, 5 β-strands

ElementResiduesLengthSheet
β-strand411
β-strand6-832
α-helix17-2610
β-strand34-3522
α-helix41-5010
β-strand54-5522
β-strand5811
Chains AB and FD: 1 helix, 7 β-strands
ElementResiduesLengthSheet
β-strand5-1063
β-strand18-2473
β-strand27-2824
β-strand35-3624
β-strand39-4573
β-strand56-6163
β-strand71-7663
α-helix82-9413
Chains AC and V: 2 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand12-1545
β-strand24-2635
β-strand27-3156
α-helix32-343
β-strand36-3946
β-strand44-4967
β-strand59-6467
α-helix65-662
β-strand67-6826
β-strand72-7435
β-strand7518
β-strand8218
β-strand86-8839
β-strand96-9839
Chain AD: 3 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix8-125
α-helix25-273
β-strand33-431110
α-helix44-463
β-strand53-60810
β-strand65-69510
β-strand82-85410
β-strand99-103510
β-strand104111
β-strand105110
β-strand107111
Chains BA and GC: 1 helix, 4 β-strands
ElementResiduesLengthSheet
β-strand13-14212
β-strand16113
β-strand20113
β-strand30-31212
α-helix59-613
Chains BB and GD: 6 helices, 3 β-strands
ElementResiduesLengthSheet
β-strand29-302134
α-helix37-404
α-helix41-433
β-strand44114
α-helix491
β-strand50114
α-helix51-522
α-helix53-564
α-helix60-7516
Chain BC: 4 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand3-6415
β-strand8-9215
α-helix15-206
β-strand23-29715
β-strand34-40715
α-helix41-5111
β-strand57-61515
β-strand64-761315
β-strand83-90815
α-helix91-922
β-strand98-101416
β-strand103-105317
β-strand116-118318
β-strand123-127516
β-strand138-140317
β-strand146118
β-strand148-151418
β-strand162-163216
β-strand170-175618
α-helix182-1876
Chain BD: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-102
α-helix31-366
α-helix52-6110
α-helix67-8418
α-helix90-934

60 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
16S ribosomal RNAA, FBRNA1507Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
23S ribosomal RNAB, GBRNA2880Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
5S ribosomal RNAC, HBRNA120Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
tRNAD, IA, IB, NCRNA77Escherichia coli K-12
50S ribosomal protein L2E, JBprotein275Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Q72I07 (AlphaFold model)
50S ribosomal protein L3F, KBprotein206Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Q72I04 (AlphaFold model)
50S ribosomal protein L4G, LBprotein205Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Q72I05 (AlphaFold model)
50S ribosomal protein L5H, MBprotein182Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Q72I16 (AlphaFold model)
50S ribosomal protein L6I, NBprotein180Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Q72I19
50S ribosomal protein L9J, OBprotein148Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Q72GV5
50S ribosomal protein L13K, PBprotein140Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Q72IN1
50S ribosomal protein L14L, QBprotein122Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Q72I14

43 more molecules are not listed.

Sequence of entity 1 (A, FB), FASTA
>6BOH_1 16S ribosomal RNA (chains A, FB)
UUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUC
GUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUG
ACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCG
CCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGC
UAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCC
GGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUU
CCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUG
UAAACUCCUGAACCCGGGACGAAACCCCCGAGGAGGGGACUGACGGUACCGGGGUAAUAG
CGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAU
UCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUC
AACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCC
CGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCU
GGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGG
UAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAAC
GCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGG
GGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCA
GGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUA
GCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCA
ACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGC
CCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGG
CGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUC
GCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUC
GCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCG
CCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCC
GAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGG
CUGGAUC
Sequence of entity 2 (B, GB), FASTA
>6BOH_2 23S ribosomal RNA (chains B, GB)
AGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGCUACC
UGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGGGGAA
CCCGGCCGGCGGGAACGCCGGUCACCGCGCCUUUUUGCGCGGGGGGAACCUGGGGAACUG
AAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAGCG
AAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGACAC
CGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCCGU
AGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCAUG
GGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCACCA
GUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAACCG
UGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGAGC
CGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCGAG
UCCGAACAGGGCGUCUAGUCCGCGGCCGUGGACCCGAAACCGGGCGAGCUAGCCCUGGCC
AGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGAACCGGUGGGGGAUGCAAACCCCUC
GGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAGCCCGGAGAUAGCUGGUUCUCCCCG
AAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGGGCCUGUAGAGCACUGAUAGGGCUA
GGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCCGAAGGGUCCCAGGUGGAGCCUGGG
AGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCGCGGGAACAACCGAGACCGCCAGCU
AAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGUGGCGCCGCGAAGACAGCCAGGAGG
UUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGGCGCC
GCGCCGAAAAUGAUCGGGGCUCAAGCCCAGCGCCGAAGCUGCGGGUCUGGGGGAUGACCC
CAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGGCGGCUGGAGG
UAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAAAGAGGGUGAGAAUCCCUCUCGCCG
UAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGUAGGGUUAGGCGGGACCUAAGGUGA
AGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUAUUCCGGCCCUUCCCGCAGGUGCGA
UGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAUGGACGAGCCCGGCCAGAAGCGCAG
GGUGGGAGGUAGGCAAAUCCGCCUCCCAAAAGCUCUGCGUGGUGGGGAAGCCCGUACGGG
UGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGCCUCUAAGCACAACCUGCGGGAACCC
GUACCGCAAACCGACACAGGUGGGCGGGUGCAAGAGCACUCAGGCGCGCGGGAGAACCCU
CGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUCGGGAGAAGGGGUGCUCCCUGGGGUG
AUGAGCUCCGGGGAGCCGCAGUGAACAGGCUCUGGCGACUGUUUACCAAAAACACAGCUC
UCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGACGCUUGCCCGGUGCCGGAAGGUCAAG
GGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUC
CUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAAGCGUAACGACCG
GAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGAACUGGCCGUGAAGAUGCGGCCUACC
CGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACUGCAGCCUGGUGUUGGCUCUUGGUCG
CGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGGCGCC
GGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAACCCUCGGAUGGGGGGACAGCGCUUG
GCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUCCC
CUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAGGGUAGAAGGGGGCCUGACUGCGAGG
CCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAGUGAACCGGUGGUCCCGUGUGGAAGG
GCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGCGUC
CACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAA
GGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUC
GUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCAGGAGGCUUGAGGGGGGCUCUUCCUA
GUACGAGAGGACCGGAAGGGACGCACCUCUGGUUUCCCAGCUGUCCCUCCAGGGGCAUAA
GCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCCGCCC
CAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAGGACCCGGGAAGACGACCCGGUGGAU
GGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCCGACCGGUCCCAAUCGUCCGAGGUCU
Sequence of entity 3 (C, HB), FASTA
>6BOH_3 5S ribosomal RNA (chains C, HB)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
Sequence of entity 4 (D, IA, IB, NC), FASTA
>6BOH_4 tRNA (chains D, IA, IB, NC)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA
Sequence of entity 5 (E, JB), FASTA
>6BOH_5 50S ribosomal protein L2 (chains E, JB)
AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKRL
YRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAGP
DAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSGE
LRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAP
RGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK
Sequence of entity 6 (F, KB), FASTA
>6BOH_6 50S ribosomal protein L3 (chains F, KB)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK
Sequence of entity 7 (G, LB), FASTA
>6BOH_7 50S ribosomal protein L4 (chains G, LB)
MYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIW
PQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLL
VEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYD
IVRTERLVMDLDAWEVFQNRIGGEA
Sequence of entity 8 (H, MB), FASTA
>6BOH_8 50S ribosomal protein L5 (chains H, MB)
MPLDLALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK
Sequence of entity 9 (I, NB), FASTA
>6BOH_9 50S ribosomal protein L6 (chains I, NB)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK
Sequence of entity 10 (J, OB), FASTA
>6BOH_10 50S ribosomal protein L9 (chains J, OB)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGITIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE
Sequence of entity 11 (K, PB), FASTA
>6BOH_11 50S ribosomal protein L13 (chains K, PB)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV
Sequence of entity 12 (L, QB), FASTA
>6BOH_12 50S ribosomal protein L14 (chains L, QB)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEVKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn10
BLSBlasticidin SC17 H26 N8 O52
MGMagnesium ionMg1428

Primary citation

Conformational Control of Translation Termination on the 70S Ribosome. Svidritskiy, E., Korostelev, A.A. Structure (2018) 26:821. DOI 10.1016/j.str.2018.04.001 · PubMed

Other PDB entries of the same protein (UniProt Q72I07 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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