5WDT: 70S ribosome-EF-Tu H84A complex with GppNHp
70S ribosome-EF-Tu H84A complex with GppNHp. Determined by electron microscopy at 3.0 Å resolution. Released 25 Apr 2018.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organism
- Escherichia coli
- Chains
- 59
- Atoms
- 155,275
- Mol. weight
- 2308 kDa
- Ligands
- FME, MG, PHE, GNP
- Released
- 25 Apr 2018
Explore 5WDT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5WDT contains 244 α-helices and 373 β-strands across 52 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 0: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 20-22 | 3 | |
| β-strand | 28-29 | 2 | 1 |
| β-strand | 36-37 | 2 | 1 |
| β-strand | 41 | 1 | 75 |
Chain 1: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-11 | 6 | 2 |
| β-strand | 19-24 | 6 | 2 |
| β-strand | 34-39 | 6 | 2 |
| β-strand | 44-51 | 8 | 2 |
Chain 2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-37 | 13 | |
Chain 3: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 7-10 | 4 | |
| β-strand | 14-15 | 2 | 15 |
| β-strand | 21-23 | 3 | 15 |
| α-helix | 24-25 | 2 | |
| α-helix | 37-42 | 6 | |
| β-strand | 47-48 | 2 | 15 |
| α-helix | 49-50 | 2 | |
| α-helix | 54-60 | 7 | |
Chain 4: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 19 |
| β-strand | 15-19 | 5 | 19 |
| β-strand | 22-26 | 5 | 19 |
| α-helix | 31-33 | 3 | |
| β-strand | 35-36 | 2 | 19 |
Chain 5: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-19 | 16 | |
| α-helix | 34-40 | 7 | |
| α-helix | 42-47 | 6 | |
| α-helix | 72-75 | 4 | |
| α-helix | 95-104 | 10 | |
| α-helix | 111-113 | 3 | |
Chain 6: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-15 | 5 | 27 |
| β-strand | 16 | 1 | 28 |
| β-strand | 21-25 | 5 | 27 |
| β-strand | 34 | 1 | 28 |
| α-helix | 46-51 | 6 | |
| α-helix | 57-64 | 8 | |
Chain b: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-26 | 3 | |
| β-strand | 31 | 1 | 45 |
| β-strand | 39 | 1 | 45 |
| α-helix | 42-61 | 20 | |
| β-strand | 66-69 | 4 | 46 |
| α-helix | 74-85 | 12 | |
| β-strand | 89-91 | 3 | 46 |
| α-helix | 103-121 | 19 | |
| α-helix | 130-147 | 18 | |
| α-helix | 150-152 | 3 | |
| β-strand | 159-162 | 4 | 46 |
| α-helix | 169-177 | 9 | |
| β-strand | 184-186 | 3 | 47 |
| β-strand | 198-200 | 3 | 47 |
| α-helix | 206-222 | 17 | |
44 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 |
|---|
| 23S rRNA | A | RNA | 2903 | Escherichia coli | |
| 5S rRNA | B | RNA | 120 | Escherichia coli | |
| 50S ribosomal protein L2 | C | protein | 271 | Escherichia coli | P60422 (AlphaFold model) |
| 50S ribosomal protein L3 | D | protein | 208 | Escherichia coli | P60438 (AlphaFold model) |
| 50S ribosomal protein L4 | E | protein | 200 | Escherichia coli | P60723 (AlphaFold model) |
| 50S ribosomal protein L5 | F | protein | 177 | Escherichia coli | P62399 (AlphaFold model) |
| 50S ribosomal protein L6 | G | protein | 174 | Escherichia coli | P0AG55 |
| 50S ribosomal protein L9 | H | protein | 149 | Escherichia coli | P0A7R1 |
| 50S ribosomal protein L11 | I | protein | 141 | Escherichia coli | P0A7J7 |
| 50S ribosomal protein L13 | J | protein | 141 | Escherichia coli | P0AA10 |
| 50S ribosomal protein L14 | K | protein | 122 | Escherichia coli | P0ADY3 |
| 50S ribosomal protein L15 | L | protein | 143 | Escherichia coli | P02413 |
46 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>5WDT_1 23S rRNA (chains A)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGGAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
AUGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUCGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAACUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGUGAAGGUGUACUGUGAGGUAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGCGACUUGCUCGUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGGAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACXAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACUCCUUGAGAGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCU
Sequence of entity 2 (B), FASTA
>5WDT_2 5S rRNA (chains B)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAA
Sequence of entity 3 (C), FASTA
>5WDT_3 50S ribosomal protein L2 (chains C)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS
Sequence of entity 4 (D), FASTA
>5WDT_4 50S ribosomal protein L3 (chains D)
IGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVT
KPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGT
VKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRVD
AERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 5 (E), FASTA
>5WDT_5 50S ribosomal protein L4 (chains E)
ELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWR
QKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVV
EKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLI
AFDKVVMTADAVKQVEEMLA
Sequence of entity 6 (F), FASTA
>5WDT_6 50S ribosomal protein L5 (chains F)
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAIS
GQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKS
FDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR
Sequence of entity 7 (G), FASTA
>5WDT_7 50S ribosomal protein L6 (chains G)
SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADG
WAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGI
TAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAK
Sequence of entity 8 (H), FASTA
>5WDT_8 50S ribosomal protein L9 (chains H)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE
Sequence of entity 9 (I), FASTA
>5WDT_9 50S ribosomal protein L11 (chains I)
AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITV
YADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGAD
IEAMTRSIEGTARSMGLVVED
Sequence of entity 10 (J), FASTA
>5WDT_10 50S ribosomal protein L13 (chains J)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLD
Sequence of entity 11 (K), FASTA
>5WDT_11 50S ribosomal protein L14 (chains K)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EV
Sequence of entity 12 (L), FASTA
>5WDT_12 50S ribosomal protein L15 (chains L)
MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRR
LPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPV
TVRGLRVTKGARAAIEAAGGKIE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| FME | N-formylmethionine | C6 H11 N O3 S | 1 |
| MG | Magnesium ion | Mg | 1904 |
| PHE | Phenylalanine | C9 H11 N O2 | 1 |
| GNP | Phosphoaminophosphonic acid-guanylate ester | C10 H17 N6 O13 P3 | 1 |
Water and common crystallization additives (K) are not listed.
Primary citation
Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A. Fislage, M., Zhang, J., Brown, Z.P. et al. Nucleic Acids Res (2018) 46:5861-5874. DOI 10.1093/nar/gky346 · PubMed
Other PDB entries of the same protein (UniProt P60422 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8B0X 1.55 Å, Translating 70S ribosome in the unrotated state (P and E, tRNAs)
- 9Q87 1.55 Å, Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom…
- 8CGK 1.64 Å, Lincomycin and Avilamycin bound to the 50S subunit
- 8CGV 1.66 Å, Tiamulin bound to the 50S subunit
- 8CEU 1.83 Å, Retapamulin and Capreomycin bound to the 50S subunit
- 8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
- 8CAM 1.86 Å, Evernimicin bound to the 50S subunit
- 9GHE 1.87 Å, Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S…
- 9T0Y 1.87 Å, E. coli 70S ribosome from delta-9 strain
- 9T6M 1.87 Å, E. coli 70S ribosome from delta-10 strain
- 9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
- 8E30 1.91 Å, E. coli 50S ribosome bound to compound streptogramin A analog 3142
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