6B4V: 50S ribosomal protein L2
Antibiotic blasticidin S and E. coli release factor 1 bound to the 70S ribosome. Determined by X-ray diffraction at 3.4 Å resolution. Released 7 Feb 2018.
- Method
- X-ray diffraction
- Resolution
- 3.4 Å
- Organisms
- Thermus thermophilus HB27, Escherichia coli K-12, synthetic construct
- Chains
- 112
- Atoms
- 299,841
- Mol. weight
- 4544.27 kDa
- Ligands
- MG, BLS, ZN
- Released
- 7 Feb 2018
Explore 6B4V in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6B4V contains 485 α-helices and 723 β-strands across 100 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.
Chains AA and EC: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 1 |
| α-helix | 17-26 | 10 | |
| β-strand | 34-37 | 4 | 1 |
| α-helix | 41-48 | 8 | |
| β-strand | 54-58 | 5 | 1 |
Chains AB and ED: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 22-25 | 4 | |
| β-strand | 29-30 | 2 | 139 |
| α-helix | 37-40 | 4 | |
| α-helix | 41-43 | 3 | |
| β-strand | 44 | 1 | 2 |
| α-helix | 49 | 1 | |
| β-strand | 50 | 1 | 2 |
| α-helix | 51-52 | 2 | |
| α-helix | 60-73 | 14 | |
| α-helix | 74-78 | 5 | |
| β-strand | 85-86 | 2 | 190 |
Chains AC and W: 6 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 3 |
| β-strand | 8-9 | 2 | 3 |
| α-helix | 15-20 | 6 | |
| α-helix | 23-24 | 2 | |
| β-strand | 25-29 | 5 | 3 |
| β-strand | 34-38 | 5 | 3 |
| α-helix | 41-51 | 11 | |
| β-strand | 56-60 | 5 | 3 |
| β-strand | 68-77 | 10 | 3 |
| β-strand | 82-90 | 9 | 3 |
| β-strand | 97-99 | 3 | 4 |
| β-strand | 102-105 | 4 | 5 |
| α-helix | 109-112 | 4 | |
| β-strand | 116-119 | 4 | 6 |
| β-strand | 125-127 | 3 | 4 |
| α-helix | 130-132 | 3 | |
| β-strand | 137-140 | 4 | 5 |
| β-strand | 149-151 | 3 | 6 |
| β-strand | 162-163 | 2 | 4 |
| β-strand | 170-175 | 6 | 6 |
| α-helix | 180-186 | 7 | |
Chains AD and WA: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| β-strand | 30 | 1 | 7 |
| β-strand | 32 | 1 | 7 |
| β-strand | 33 | 1 | 8 |
| β-strand | 40 | 1 | 8 |
| α-helix | 41-49 | 9 | |
| β-strand | 56-58 | 3 | 222 |
Chains BA and FC: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-15 | 4 | 9 |
| β-strand | 21-24 | 4 | 9 |
| α-helix | 59-61 | 3 | |
Chains BB and FD: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-17 | 3 | |
| α-helix | 42-44 | 3 | |
| β-strand | 48 | 1 | 10 |
| β-strand | 61 | 1 | 10 |
Chains BC and X: 2 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| β-strand | 22-23 | 2 | 11 |
| β-strand | 30-31 | 2 | 12 |
| β-strand | 36-39 | 4 | 11 |
| β-strand | 46-47 | 2 | 13 |
| β-strand | 51-53 | 3 | 11 |
| β-strand | 59-61 | 3 | 11 |
| β-strand | 65-66 | 2 | 12 |
| β-strand | 67-71 | 5 | 13 |
| α-helix | 73-75 | 3 | |
| β-strand | 77-81 | 5 | 13 |
Chains BD and XA: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 25-42 | 18 | |
| α-helix | 50-73 | 24 | |
| α-helix | 75-84 | 10 | |
60 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 |
|---|
| 16S ribosomal RNA | A, EB | RNA | 1507 | Thermus thermophilus HB27 | |
| 23S ribosomal RNA | B, FB | RNA | 2880 | Thermus thermophilus HB27 | |
| 5S ribosomal RNA | C, GB | RNA | 120 | Thermus thermophilus HB27 | |
| tRNA | D, HB, IA, MC | RNA | 77 | Escherichia coli K-12 | |
| 50S ribosomal protein L2 | E, IB | protein | 275 | Thermus thermophilus HB27 | Q72I07 (AlphaFold model) |
| 50S ribosomal protein L3 | F, JB | protein | 206 | Thermus thermophilus HB27 | Q72I04 (AlphaFold model) |
| 50S ribosomal protein L4 | G, KB | protein | 205 | Thermus thermophilus HB27 | Q72I05 (AlphaFold model) |
| 50S ribosomal protein L5 | H, LB | protein | 182 | Thermus thermophilus HB27 | Q72I16 (AlphaFold model) |
| 50S ribosomal protein L6 | I, MB | protein | 180 | Thermus thermophilus HB27 | Q72I19 |
| 50S ribosomal protein L9 | J, NB | protein | 148 | Thermus thermophilus HB27 | Q72GV5 |
| 50S ribosomal protein L13 | K, OB | protein | 140 | Thermus thermophilus HB27 | Q72IN1 |
| 50S ribosomal protein L14 | L, PB | protein | 122 | Thermus thermophilus HB27 | Q72I14 |
43 more molecules are not listed.
Sequence of entity 1 (A, EB), FASTA
>6B4V_1 16S ribosomal RNA (chains A, EB)
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, FB), FASTA
>6B4V_2 23S ribosomal RNA (chains B, FB)
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, GB), FASTA
>6B4V_3 5S ribosomal RNA (chains C, GB)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
Sequence of entity 4 (D, HB, IA, MC), FASTA
>6B4V_4 tRNA (chains D, HB, IA, MC)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA
Sequence of entity 5 (E, IB), FASTA
>6B4V_5 50S ribosomal protein L2 (chains E, IB)
AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKRL
YRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAGP
DAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSGE
LRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAP
RGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK
Sequence of entity 6 (F, JB), FASTA
>6B4V_6 50S ribosomal protein L3 (chains F, JB)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK
Sequence of entity 7 (G, KB), FASTA
>6B4V_7 50S ribosomal protein L4 (chains G, KB)
MYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIW
PQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLL
VEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYD
IVRTERLVMDLDAWEVFQNRIGGEA
Sequence of entity 8 (H, LB), FASTA
>6B4V_8 50S ribosomal protein L5 (chains H, LB)
MPLDLALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK
Sequence of entity 9 (I, MB), FASTA
>6B4V_9 50S ribosomal protein L6 (chains I, MB)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK
Sequence of entity 10 (J, NB), FASTA
>6B4V_10 50S ribosomal protein L9 (chains J, NB)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGITIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE
Sequence of entity 11 (K, OB), FASTA
>6B4V_11 50S ribosomal protein L13 (chains K, OB)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV
Sequence of entity 12 (L, PB), FASTA
>6B4V_12 50S ribosomal protein L14 (chains L, PB)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEVKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1683 |
| BLS | Blasticidin S | C17 H26 N8 O5 | 2 |
| ZN | Zinc ion | Zn | 10 |
Primary citation
Mechanism of Inhibition of Translation Termination by Blasticidin S. Svidritskiy, E., Korostelev, A.A. J Mol Biol (2018) 430:591-593. DOI 10.1016/j.jmb.2018.01.007 · PubMed
Other PDB entries of the same protein (UniProt Q72I07 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5J4D 3.1 Å, E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated…
- 6N1D 3.2 Å, X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into…
- 4V63 3.21 Å, Structural basis for translation termination on the 70S ribosome.
- 5V8I 3.25 Å, Thermus thermophilus 70S ribosome lacking ribosomal protein uS17
- 4V84 3.4 Å, Crystal structure of a complex containing domain 3 of CrPV IGR IRES RNA bound to the 70S…
- 4V9N 3.4 Å, Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.
- 4V9Q 3.4 Å, Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome.
- 6BOH 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304)…
- 4V83 3.5 Å, Crystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to…
- 4V9K 3.5 Å, 70S ribosome translocation intermediate GDPNP-I containing elongation factor EFG/GDPNP,…
- 4V9L 3.5 Å, 70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC…
- 6BOK 3.55 Å, E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome
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