5OT7: 50S ribosomal protein L25

Elongation factor G-ribosome complex captures in the absence of inhibitors. Determined by electron microscopy at 3.8 Å resolution. Released 14 Feb 2018.

Method
Electron microscopy
Resolution
3.8 Å
Organisms
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), Escherichia coli
Chains
59
Atoms
154,665
Mol. weight
2303.76 kDa
Ligands
MG, ZN, GDP
Released
14 Feb 2018

Explore 5OT7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OT7 contains 234 α-helices and 331 β-strands across 54 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 6: 2 helices, 10 β-strands

ElementResiduesLengthSheet
β-strand5128
β-strand23-28628
β-strand35-40628
α-helix41-477
β-strand57-60428
β-strand66-761128
β-strand83-90828
β-strand96-98329
β-strand103-105330
α-helix111-1133
β-strand126-128329
β-strand138-140330
Chain 7: 8 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand3-5334
β-strand19134
α-helix23-253
α-helix26-305
β-strand36-38334
α-helix43-497
α-helix55-584
α-helix59-635
α-helix82-843
α-helix100-1034
β-strand125-128435
α-helix136-1372
β-strand138-141435
Chain a: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix13-197
α-helix25-295
β-strand31-32240
α-helix331
β-strand39-40240
α-helix50-534
Chain A: 9 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix41-433
α-helix45-6218
β-strand69-71339
α-helix78-8811
α-helix105-11814
α-helix119-1213
α-helix126-1294
α-helix132-14514
β-strand162-164339
α-helix171-1733
β-strand184-186339
β-strand199-200239
α-helix208-22316
Chain b: 0 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand14147
β-strand37-38248
β-strand48-49248
β-strand50147
Chain B: 8 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix37-437
α-helix47-493
β-strand55-56241
β-strand59-60242
β-strand63-66442
β-strand67-68241
β-strand69-70243
α-helix73-764
α-helix90-934
β-strand99-101342
β-strand104-105243
α-helix113-1153
α-helix123-1253
α-helix132-1365
α-helix139-1446
β-strand149-150244
β-strand154-155245
β-strand164-165245
β-strand169-170244
β-strand182-183246
β-strand202-203246
Chain c: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-168
α-helix18-225
α-helix27-3711
α-helix45-473
Chain C: 11 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix10-156
α-helix24-274
α-helix49-524
α-helix53-6513
α-helix76-849
α-helix89-979
β-strand100149
α-helix103-1086
α-helix114-1229
β-strand127-128250
β-strand131-132250
β-strand139149
α-helix140-1412
β-strand144-147450
α-helix152-1543
β-strand175-177350
β-strand182-185450
α-helix201-2077

46 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 RNA1RNA1507Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
tRNA-Phe2RNA76Escherichia coli
mRNA3RNA15Escherichia coli
23S Ribosomal RNA4RNA2901Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
5S Ribosomal RNA5RNA119Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
50S ribosomal protein L256protein178Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Q5SHZ1 (AlphaFold model)
50S ribosomal protein L97protein146Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Q5SLQ1 (AlphaFold model)
30S ribosomal protein S2Aprotein235Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)P80371 (AlphaFold model)
30S ribosomal protein S3Bprotein207Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)P80372 (AlphaFold model)
30S ribosomal protein S4Cprotein208Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)P80373
30S ribosomal protein S5Dprotein151Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Q5SHQ5
30S ribosomal protein S6Eprotein101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Q5SLP8

47 more molecules are not listed.

Sequence of entity 1 (1), FASTA
>5OT7_1 16S Ribosomal RNA (chains 1)
UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCG
UGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGA
CCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGC
CCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCU
AGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCG
GCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUC
CGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGU
AAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGC
GCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUU
CACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCA
ACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCC
GGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUG
GUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGU
AGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACG
CGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGG
GGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAG
GCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAG
CACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAA
CGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCC
CGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGC
GACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCG
CAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCG
CUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGC
CCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCG
AGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGC
UGGAUCA
Sequence of entity 2 (2), FASTA
>5OT7_2 tRNA-Phe (chains 2)
GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUU
CCGAGUCCGGGCACCA
Sequence of entity 3 (3), FASTA
>5OT7_3 mRNA (chains 3)
AGGAGGUGAGGUUUU
Sequence of entity 4 (4), FASTA
>5OT7_4 23S Ribosomal RNA (chains 4)
AGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGCUACC
UGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGGGGAA
CCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUGCGCGGGGGGAACCUGGGGAACUGAA
ACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAGCGAA
AGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGACACCG
AAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCCGUAG
GCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCAUGGG
GGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCACCAGU
ACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAACCGUG
GGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGAGCCG
GCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCGAGUC
CGAACAGGGCGCAAGCGGGCCGCACGCGGCCCGCAAAGUCCGCGGCCGUGGACCCGAAAC
CGGGCGAGCUAGCCCUGGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGAACCG
GUGGGGGAUGCAAACCCCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAGCCCG
GAGAUAGCUGGUUCUCCCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGGGCCU
GUAGAGCACUGAUAGGGCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCCGAAG
GGUCCCAGGUGGAGCCUGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCGCGGG
AACAACCGAGACCGCCAGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGUGGCG
CGGCGAAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAAUAG
CUCACUGGUCGAGUGGCGCCGCGCCGAAAAUGAUCGGGGCUUAAGCCCAGCGCCGAAGCU
GCGGGUCUGGGGGAUGACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGGCCGA
CCCGCGAGGGCGGCUGGAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAAAGAG
GGUGAGAAUCCCUCUCGCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGUAGGG
UUAGGCGGGACCUAAGGUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUAUUCC
GGCCCUUCCCGCAGGUGCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAUGGAC
GAGCCCGGCCAGAAGCGCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAACAAGCUCUGCG
UGGUGGGGAAGCCCGUACGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGCCUCU
AAGCACAACCUGCGGGAACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGAGCAC
UCAGGCGCGCGGGAGAACCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUCGGGA
GAAGGGGUGCUCCCUGGGGUGAUGAGCCCCGGGGAGCCGCAGUGAACAGGCUCUGGCGAC
UGUUUACCAAAAACACAGCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGACGCUU
GCCCGGUGCCGGAAGGUCAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUGAACG
GCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCU
GCACGAAAAGCGUAACGACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGAACUG
GCCGUGAAGAUGCGGCCUACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACUGCAG
CCUGGUGUUGGCUCUUGGUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUAAACCCCCGCC
UCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAACCCU
CGGAUGGGGGGACAGCGCUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUA
ACGGAGGCGCCCAAAGGUCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAGGGUA
GAAGGGGGCCUGACUGCGAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAGUGAA
CCGGUGGUCCCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACA
GGCUGAUCUCCCCCGAGCGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCG
UCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCAC
GCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCAGGAG
GCUUGAGGGGGGCUCUUCCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUUCCCA
GCUGUCCCUCCAGGGGCAUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGAAAGC
AUCUAAGCGGGAAGCCCGCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAGGACC
CGGGAAGACCACCCGGUGGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCCGACC
GGUCCCAAUCGUCCGAGGUCU
Sequence of entity 5 (5), FASTA
>5OT7_5 5S Ribosomal RNA (chains 5)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGG
Sequence of entity 6 (6), FASTA
>5OT7_6 50S ribosomal protein L25 (chains 6)
YRLKAYYREGEKPSALRRAGKLPGVMYNRHLNRKVYVDLVEFDKVFRQASIHHVIVLELP
DGQSLPTLVRQVNLDKRRRRPEHVDFFVLSDEPVEMYVPLRFVGTPAGVRAGGVLQEIHR
DILVKVSPRNIPEFIEVDVSGLEIGDSLHASDLKLPPGVELAVSPEETIAAVVPPEDV
Sequence of entity 7 (7), FASTA
>5OT7_7 50S ribosomal protein L9 (chains 7)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVA
Sequence of entity 8 (A), FASTA
>5OT7_8 30S ribosomal protein S2 (chains A)
VKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGG
TILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPE
IEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIA
LADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQE
Sequence of entity 9 (B), FASTA
>5OT7_9 30S ribosomal protein S3 (chains B)
GNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAA
DNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVA
EQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRAN
IDYGFALARTTYGVLGVKAYIFLGEVI
Sequence of entity 10 (C), FASTA
>5OT7_10 30S ribosomal protein S4 (chains C)
GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREK
QKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLV
RHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGM
KGKFLRLPDREDLALPVNEQLVIEFYSR
Sequence of entity 11 (D), FASTA
>5OT7_11 30S ribosomal protein S5 (chains D)
DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARR
NMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELG
SRNPINIAYATMEALRQLRTKADVERLRKGE
Sequence of entity 12 (E), FASTA
>5OT7_12 30S ribosomal protein S6 (chains E)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg462
ZNZinc ionZn3
GDPGuanosine-5'-diphosphateC10 H15 N5 O11 P21

Primary citation

The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors. Mace, K., Giudice, E., Chat, S. et al. Nucleic Acids Res (2018) 46:3211-3217. DOI 10.1093/nar/gky081 · PubMed

Other PDB entries of the same protein (UniProt Q5SHZ1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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