6BOK: E. coli release factor 1
E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome. Determined by X-ray diffraction at 3.55 Å resolution. Released 23 May 2018.
- Method
- X-ray diffraction
- Resolution
- 3.55 Å
- Organisms
- Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039), synthetic construct, Escherichia coli
- Chains
- 112
- Atoms
- 299,566
- Mol. weight
- 4541.33 kDa
- Ligands
- MG, ZN
- Released
- 23 May 2018
Explore 6BOK in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6BOK contains 493 α-helices and 691 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 DC: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-8 | 6 | 1 |
| α-helix | 17-26 | 10 | |
| β-strand | 34-38 | 5 | 1 |
| α-helix | 41-47 | 7 | |
| α-helix | 51-53 | 3 | |
| β-strand | 54-59 | 6 | 1 |
Chains AB and DD: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-10 | 3 | |
| α-helix | 13-22 | 10 | |
| β-strand | 30-33 | 4 | 2 |
| β-strand | 39 | 1 | 3 |
| β-strand | 48-52 | 5 | 2 |
| β-strand | 57-61 | 5 | 2 |
| α-helix | 62 | 1 | |
| β-strand | 70 | 1 | 3 |
| α-helix | 71-74 | 4 | |
Chains AC and X: 1 helix, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-23 | 2 | 4 |
| β-strand | 30-31 | 2 | 5 |
| β-strand | 36-39 | 4 | 4 |
| β-strand | 46-47 | 2 | 5 |
| β-strand | 51-53 | 3 | 4 |
| β-strand | 59-61 | 3 | 4 |
| β-strand | 65-71 | 7 | 5 |
| α-helix | 73-75 | 3 | |
| β-strand | 77-83 | 7 | 5 |
Chain AD: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 6 |
| β-strand | 10-11 | 2 | 7 |
| β-strand | 14-15 | 2 | 7 |
| β-strand | 17-23 | 7 | 6 |
| β-strand | 34-39 | 6 | 6 |
| β-strand | 49 | 1 | 6 |
| α-helix | 53-62 | 10 | |
| α-helix | 64 | 1 | |
| β-strand | 65-66 | 2 | 6 |
| α-helix | 67 | 1 | |
| α-helix | 68-77 | 10 | |
Chains BA and EC: 1 helix, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-8 | 2 | |
| β-strand | 11-15 | 5 | 8 |
| β-strand | 21-25 | 5 | 8 |
| β-strand | 30-32 | 3 | 8 |
Chains BB and ED: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-44 | 33 | |
| α-helix | 49-67 | 19 | |
| α-helix | 74-94 | 21 | |
Chains BC and Y: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-20 | 8 | 9 |
| β-strand | 34-42 | 9 | 9 |
| β-strand | 46-53 | 8 | 10 |
| β-strand | 56-63 | 8 | 10 |
| α-helix | 64-66 | 3 | |
| α-helix | 67-77 | 11 | |
| α-helix | 87-96 | 10 | |
Chains BD and YA: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-12 | 8 | 11 |
| β-strand | 18-28 | 11 | 11 |
| β-strand | 35-45 | 11 | 11 |
| β-strand | 56-61 | 6 | 11 |
| β-strand | 71-78 | 8 | 11 |
| α-helix | 82-93 | 12 | |
| α-helix | 95-97 | 3 | |
63 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, DB | RNA | 1507 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | |
| 23S ribosomal RNA | B, EB | RNA | 2880 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | |
| 5S ribosomal RNA | C, FB | RNA | 120 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | |
| 16S ribosomal RNA | D, GB, IA, LC | RNA | 77 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | |
| 50S ribosomal protein L2 | E, HB | protein | 275 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | Q72I07 (AlphaFold model) |
| 50S ribosomal protein L3 | F, IB | protein | 206 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | Q72I04 (AlphaFold model) |
| 50S ribosomal protein L4 | G, JB | protein | 205 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | Q72I05 (AlphaFold model) |
| 50S ribosomal protein L5 | H, KB | protein | 182 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | Q72I16 (AlphaFold model) |
| 50S ribosomal protein L6 | I, LB | protein | 180 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | Q72I19 |
| 50S ribosomal protein L9 | J, MB | protein | 148 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | Q72GV5 |
| 50S ribosomal protein L13 | K, NB | protein | 140 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | Q72IN1 |
| 50S ribosomal protein L14 | L, OB | protein | 122 | Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) | Q72I14 |
43 more molecules are not listed.
Sequence of entity 1 (A, DB), FASTA
>6BOK_1 16S ribosomal RNA (chains A, DB)
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, EB), FASTA
>6BOK_2 23S ribosomal RNA (chains B, EB)
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, FB), FASTA
>6BOK_3 5S ribosomal RNA (chains C, FB)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
Sequence of entity 4 (D, GB, IA, LC), FASTA
>6BOK_4 16S ribosomal RNA (chains D, GB, IA, LC)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA
Sequence of entity 5 (E, HB), FASTA
>6BOK_5 50S ribosomal protein L2 (chains E, HB)
AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKRL
YRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAGP
DAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSGE
LRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAP
RGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK
Sequence of entity 6 (F, IB), FASTA
>6BOK_6 50S ribosomal protein L3 (chains F, IB)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK
Sequence of entity 7 (G, JB), FASTA
>6BOK_7 50S ribosomal protein L4 (chains G, JB)
MYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIW
PQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLL
VEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYD
IVRTERLVMDLDAWEVFQNRIGGEA
Sequence of entity 8 (H, KB), FASTA
>6BOK_8 50S ribosomal protein L5 (chains H, KB)
MPLDLALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK
Sequence of entity 9 (I, LB), FASTA
>6BOK_9 50S ribosomal protein L6 (chains I, LB)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK
Sequence of entity 10 (J, MB), FASTA
>6BOK_10 50S ribosomal protein L9 (chains J, MB)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGITIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE
Sequence of entity 11 (K, NB), FASTA
>6BOK_11 50S ribosomal protein L13 (chains K, NB)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV
Sequence of entity 12 (L, OB), FASTA
>6BOK_12 50S ribosomal protein L14 (chains L, OB)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEVKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1518 |
| ZN | Zinc ion | Zn | 10 |
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:
- 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.
- 6B4V 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 bound to the 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…
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