5U4I: Co-translational Quality Control by ArfA and RF2
Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome. Determined by electron microscopy at 3.5 Å resolution. Released 11 Jan 2017.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organisms
- Escherichia coli, Escherichia coli (strain K12)
- Chains
- 57
- Atoms
- 149,495
- Mol. weight
- 2249.3 kDa
- Ligands
- MG, ZN
- Released
- 11 Jan 2017
Explore 5U4I in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5U4I contains 245 α-helices and 311 β-strands across 51 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 |
|---|
| β-strand | 5-9 | 5 | 93 |
| α-helix | 18-27 | 10 | |
| β-strand | 35-38 | 4 | 93 |
| α-helix | 42-50 | 9 | |
| β-strand | 55-58 | 4 | 93 |
Chain 1: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| α-helix | 10-20 | 11 | |
| α-helix | 22-25 | 4 | |
| β-strand | 29-30 | 2 | 1 |
| β-strand | 37-38 | 2 | 1 |
| β-strand | 42 | 1 | 62 |
| β-strand | 48 | 1 | 2 |
| β-strand | 53 | 1 | 2 |
Chain 2: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-13 | 7 | 5 |
| β-strand | 20-25 | 6 | 5 |
| β-strand | 36-40 | 5 | 5 |
| β-strand | 45-50 | 6 | 5 |
Chain 3: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-23 | 6 | |
| α-helix | 25-37 | 13 | |
Chain 4: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-13 | 6 | |
| β-strand | 15-16 | 2 | 17 |
| β-strand | 22-24 | 3 | 17 |
| α-helix | 38-44 | 7 | |
| β-strand | 48-49 | 2 | 17 |
| α-helix | 50-51 | 2 | |
| α-helix | 54-61 | 8 | |
Chain 5: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 20 |
| β-strand | 14-19 | 6 | 20 |
| β-strand | 22-27 | 6 | 20 |
| β-strand | 35-37 | 3 | 20 |
Chain b: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-12 | 7 | |
| β-strand | 16-19 | 4 | 27 |
| α-helix | 25-30 | 6 | |
| β-strand | 31-35 | 5 | 27 |
| β-strand | 38-41 | 4 | 27 |
| α-helix | 47-62 | 16 | |
| β-strand | 67-70 | 4 | 28 |
| α-helix | 74-87 | 14 | |
| β-strand | 90-92 | 3 | 28 |
| α-helix | 95-97 | 3 | |
| α-helix | 104-122 | 19 | |
| α-helix | 131-147 | 17 | |
| α-helix | 151-154 | 4 | |
| β-strand | 160-163 | 4 | 28 |
| α-helix | 170-179 | 10 | |
| β-strand | 183-186 | 4 | 28 |
| β-strand | 198-200 | 3 | 28 |
| α-helix | 207-226 | 20 | |
Chain c: 9 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| α-helix | 17-18 | 2 | |
| β-strand | 20 | 1 | 32 |
| α-helix | 26-28 | 3 | |
| α-helix | 30-46 | 17 | |
| β-strand | 52-58 | 7 | 32 |
| β-strand | 64-70 | 7 | 32 |
| α-helix | 73-76 | 4 | |
| α-helix | 82-95 | 14 | |
| β-strand | 99-105 | 7 | 32 |
| α-helix | 106 | 1 | |
| α-helix | 113-125 | 13 | |
| α-helix | 130-144 | 15 | |
| β-strand | 148-154 | 7 | 33 |
| β-strand | 165-171 | 7 | 33 |
| β-strand | 180-190 | 11 | 33 |
| β-strand | 195-206 | 12 | 33 |
43 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 | 2904 | Escherichia coli | |
| 5S rRNA | B | RNA | 118 | Escherichia coli | |
| 50S ribosomal protein L2 | C | protein | 273 | Escherichia coli (strain K12) | P60422 (AlphaFold model) |
| 50S ribosomal protein L3 | D | protein | 209 | Escherichia coli (strain K12) | P60438 (AlphaFold model) |
| 50S ribosomal protein L4 | E | protein | 201 | Escherichia coli (strain K12) | P60723 (AlphaFold model) |
| 50S ribosomal protein L5 | F | protein | 179 | Escherichia coli (strain K12) | P62399 (AlphaFold model) |
| 50S ribosomal protein L6 | G | protein | 177 | Escherichia coli (strain K12) | P0AG55 |
| 50S ribosomal protein L9 | H | protein | 149 | Escherichia coli (strain K12) | P0A7R1 |
| 50S ribosomal protein L11 | J | protein | 142 | Escherichia coli (strain K12) | P0A7J7 |
| 50S ribosomal protein L13 | K | protein | 142 | Escherichia coli (strain K12) | P0AA10 |
| 50S ribosomal protein L14 | L | protein | 123 | Escherichia coli (strain K12) | P0ADY3 |
| 50S ribosomal protein L15 | M | protein | 144 | Escherichia coli (strain K12) | P02413 |
44 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>5U4I_1 23S rRNA (chains A)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAACCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCUU
Sequence of entity 2 (B), FASTA
>5U4I_2 5S rRNA (chains B)
GCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACG
CCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCA
Sequence of entity 3 (C), FASTA
>5U4I_3 50S ribosomal protein L2 (chains C)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK
Sequence of entity 4 (D), FASTA
>5U4I_4 50S ribosomal protein L3 (chains D)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 5 (E), FASTA
>5U4I_5 50S ribosomal protein L4 (chains E)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 6 (F), FASTA
>5U4I_6 50S ribosomal protein L5 (chains F)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK
Sequence of entity 7 (G), FASTA
>5U4I_7 50S ribosomal protein L6 (chains G)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK
Sequence of entity 8 (H), FASTA
>5U4I_8 50S ribosomal protein L9 (chains H)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE
Sequence of entity 9 (J), FASTA
>5U4I_9 50S ribosomal protein L11 (chains J)
MAKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVIT
VYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGA
DIEAMTRSIEGTARSMGLVVED
Sequence of entity 10 (K), FASTA
>5U4I_10 50S ribosomal protein L13 (chains K)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI
Sequence of entity 11 (L), FASTA
>5U4I_11 50S ribosomal protein L14 (chains L)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EVL
Sequence of entity 12 (M), FASTA
>5U4I_12 50S ribosomal protein L15 (chains M)
MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRR
LPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPV
TVRGLRVTKGARAAIEAAGGKIEE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 124 |
| ZN | Zinc ion | Zn | 1 |
Primary citation
Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome. Zeng, F., Chen, Y., Remis, J. et al. Nature (2017) 541:554-557. DOI 10.1038/nature21053 · 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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