5U4J: 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 3.7 Å resolution. Released 11 Jan 2017.
- Method
- Electron microscopy
- Resolution
- 3.7 Å
- Organism
- Escherichia coli
- Chains
- 10
- Atoms
- 11,360
- Mol. weight
- 1600.33 kDa
- Released
- 11 Jan 2017
Explore 5U4J in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5U4J contains 17 α-helices and 27 β-strands across 6 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 c: 0 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 151-155 | 5 | 1 |
| β-strand | 164-168 | 5 | 1 |
Chain d: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-15 | 8 | |
| α-helix | 28-31 | 4 | |
| α-helix | 37 | 1 | |
| α-helix | 50-64 | 15 | |
Chain e: 3 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-24 | 13 | 2 |
| β-strand | 29-40 | 12 | 2 |
| β-strand | 45-46 | 2 | 3 |
| β-strand | 47-50 | 4 | 2 |
| β-strand | 53 | 1 | 2 |
| α-helix | 56-68 | 13 | |
| β-strand | 72-73 | 2 | 3 |
| β-strand | 80 | 1 | 4 |
| β-strand | 85-89 | 5 | 5 |
| β-strand | 92-98 | 7 | 5 |
| β-strand | 105-106 | 2 | 5 |
| α-helix | 109-118 | 10 | |
| β-strand | 122 | 1 | 4 |
| β-strand | 123-128 | 6 | 5 |
| α-helix | 133-144 | 12 | |
Chain l: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| β-strand | 30-40 | 11 | 6 |
| α-helix | 41-42 | 2 | |
| β-strand | 50-57 | 8 | 6 |
| β-strand | 62-66 | 5 | 6 |
| β-strand | 79-83 | 5 | 6 |
| β-strand | 95-97 | 3 | 6 |
| α-helix | 104-107 | 4 | |
| α-helix | 120-122 | 3 | |
Chain v: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 129-135 | 7 | 7 |
| α-helix | 140-159 | 20 | |
| β-strand | 164-170 | 7 | 7 |
| β-strand | 176-182 | 7 | 7 |
| α-helix | 188-191 | 4 | |
| β-strand | 197-204 | 8 | 7 |
| β-strand | 213-223 | 11 | 7 |
| α-helix | 297-315 | 19 | |
| β-strand | 322-326 | 5 | 7 |
Chain w: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4 | 1 | 6 |
| α-helix | 15-20 | 6 | |
| α-helix | 23-25 | 3 | |
| β-strand | 28-29 | 2 | 7 |
| α-helix | 30 | 1 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 16S rRNA | a | RNA | 1533 | Escherichia coli | |
| 23S rRNA | A | RNA | 2904 | Escherichia coli | |
| 30S ribosomal protein S3 | c | protein | 233 | Escherichia coli | P0A7V3 (AlphaFold model) |
| 30S ribosomal protein S4 | d | protein | 206 | Escherichia coli | P0A7V8 (AlphaFold model) |
| 30S ribosomal protein S5 | e | protein | 167 | Escherichia coli | P0A7W1 (AlphaFold model) |
| mRNA | z | RNA | 18 | Escherichia coli | |
| P-site tRNA fMet | x | RNA | 77 | Escherichia coli | |
| 30S ribosomal protein S12 | l | protein | 124 | Escherichia coli | P0A7S3 (AlphaFold model) |
| Peptide chain release factor 2 | v | protein | 383 | Escherichia coli | P07012 |
| Alternative ribosome-rescue factor A | w | protein | 57 | Escherichia coli | P36675 |
Sequence of entity 1 (a), FASTA
>5U4J_1 16S rRNA (chains a)
AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAG
UCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAU
GUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUA
ACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGG
GAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAG
GAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGG
GAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUU
CGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUG
ACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGG
GUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAG
AUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCG
UAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCG
GUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAA
ACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCC
UUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAA
GGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUU
CGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGA
AUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAA
AUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCC
GGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA
UCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGA
CCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACU
CGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUU
CCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUA
GCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAAC
AAGGUAACCGUAGGGGAACCUGCGGUUGGAUCA
Sequence of entity 2 (A), FASTA
>5U4J_2 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 3 (c), FASTA
>5U4J_3 30S ribosomal protein S3 (chains c)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK
Sequence of entity 4 (d), FASTA
>5U4J_4 30S ribosomal protein S4 (chains d)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK
Sequence of entity 5 (e), FASTA
>5U4J_5 30S ribosomal protein S5 (chains e)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK
Sequence of entity 6 (z), FASTA
>5U4J_6 mRNA (chains z)
GGCAAGGAGGUAAAAAUG
Sequence of entity 7 (x), FASTA
>5U4J_7 P-site tRNA fMet (chains x)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA
Sequence of entity 8 (l), FASTA
>5U4J_8 30S ribosomal protein S12 (chains l)
MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNG
FEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVK
RPKA
Sequence of entity 9 (v), FASTA
>5U4J_9 Peptide chain release factor 2 (chains v)
HHHHHHSAALEVLFQGPGMFEINPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELE
QPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAE
LDALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFK
TEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFV
YPEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHK
NKDQAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVET
RNTQAVLDGSLDQFIEASLKAGL
Sequence of entity 10 (w), FASTA
>5U4J_10 Alternative ribosome-rescue factor A (chains w)
GSMSRYQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYMRKGKHGNRGNWEASG
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 P0A7V3 (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…
- 8CGJ 1.79 Å, Streptomycin bound to the 30S body
- 8CF1 1.82 Å, Tetracycline bound to the 30S head
- 8FTO 1.85 Å, E. coli 70S ribosome with an improved MS2 tag inserted in H98
- 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
- 8CGI 1.89 Å, Pentacycline TP038 bound to the 30S head
- 9SYH 1.89 Å, E. coli 70S ribosome from deltaRlmE strain
- 8AYE 1.96 Å, E. coli 70S ribosome bound to thermorubin and fMet-tRNA
- 7K00 1.98 Å, Structure of the Bacterial Ribosome at 2 Angstrom Resolution
Browse structure collections
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