5J4D: E. coli release factor 1

E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated stop codon. Determined by X-ray diffraction at 3.1 Å resolution. Released 18 May 2016.

Method
X-ray diffraction
Resolution
3.1 Å
Organisms
Thermus thermophilus HB27, Escherichia coli K-12, Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Chains
112
Atoms
300,991
Mol. weight
4575.46 kDa
Ligands
MG, ZN
Released
18 May 2016

Explore 5J4D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J4D contains 504 α-helices and 669 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 FC: 3 helices, 3 β-strands

ElementResiduesLengthSheet
β-strand4-851
α-helix17-2610
β-strand34-3741
α-helix41-499
α-helix51-533
β-strand54-5851
Chains AB and FD: 6 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand29-302119
α-helix37-404
α-helix41-433
β-strand4412
α-helix491
β-strand5012
α-helix51-522
α-helix53-564
α-helix60-7617
β-strand85-862160
Chains AC and V: 3 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand12-154199
β-strand24-263199
β-strand27-315200
β-strand36-394200
β-strand44-485201
β-strand60-645201
α-helix65-662
β-strand67-682200
α-helix69-713
β-strand72-743199
β-strand751202
α-helix761
β-strand821202
β-strand85-895203
β-strand95-995203
β-strand1051203
Chains AD and VA: 6 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand141204
α-helix15-206
α-helix27-359
β-strand441204
α-helix50-6314
α-helix67-8418
α-helix87-948
α-helix108-1114
Chain BA: 2 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix7-82
β-strand10-1568
β-strand21-2668
β-strand3018
α-helix59-613
Chains BB and GD: 3 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix8-103
α-helix13-2412
β-strand31-3229
β-strand39110
β-strand48-5259
β-strand57-6159
β-strand70110
α-helix71-744
Chains BC and W: 7 helices, 14 β-strands
ElementResiduesLengthSheet
β-strand2-983
α-helix15-206
β-strand23-3083
β-strand33-4083
α-helix41-5111
β-strand56-6053
β-strand66-77123
β-strand82-9093
β-strand96-10164
β-strand102-10545
α-helix109-1124
β-strand116-11836
β-strand123-12864
α-helix130-1323
β-strand137-14045
β-strand149-15136
α-helix152-1543
β-strand162-16324
β-strand170-17566
α-helix176-1783
α-helix182-1887
Chains BD and WA: 4 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix4-118
α-helix17-193
α-helix22-243
β-strand33-3427
β-strand39-4027
α-helix41-5010
β-strand57-582187

59 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 HB27
25S ribosomal RNAB, GBRNA2880Thermus thermophilus HB27
5S ribosomal RNAC, HBRNA120Thermus thermophilus HB27
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
>5J4D_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
>5J4D_2 25S 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
>5J4D_3 5S ribosomal RNA (chains C, HB)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
Sequence of entity 4 (D, IA, IB, NC), FASTA
>5J4D_4 tRNA (chains D, IA, IB, NC)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA
Sequence of entity 5 (E, JB), FASTA
>5J4D_5 50S ribosomal protein L2 (chains E, JB)
AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKRL
YRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAGP
DAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSGE
LRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAP
RGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK
Sequence of entity 6 (F, KB), FASTA
>5J4D_6 50S ribosomal protein L3 (chains F, KB)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK
Sequence of entity 7 (G, LB), FASTA
>5J4D_7 50S ribosomal protein L4 (chains G, LB)
MYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIW
PQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLL
VEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYD
IVRTERLVMDLDAWEVFQNRIGGEA
Sequence of entity 8 (H, MB), FASTA
>5J4D_8 50S ribosomal protein L5 (chains H, MB)
MPLDLALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK
Sequence of entity 9 (I, NB), FASTA
>5J4D_9 50S ribosomal protein L6 (chains I, NB)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK
Sequence of entity 10 (J, OB), FASTA
>5J4D_10 50S ribosomal protein L9 (chains J, OB)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGITIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE
Sequence of entity 11 (K, PB), FASTA
>5J4D_11 50S ribosomal protein L13 (chains K, PB)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV
Sequence of entity 12 (L, QB), FASTA
>5J4D_12 50S ribosomal protein L14 (chains L, QB)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEVKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg2893
ZNZinc ionZn10

Primary citation

Structural Basis for Translation Termination on a Pseudouridylated Stop Codon. Svidritskiy, E., Madireddy, R., Korostelev, A.A. J Mol Biol (2016) 428:2228-2236. DOI 10.1016/j.jmb.2016.04.018 · 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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