5MGP: 50S ribosomal protein L2
Structural basis for ArfA-RF2 mediated translation termination on stop-codon lacking mRNAs. Determined by electron microscopy at 3.1 Å resolution. Released 14 Dec 2016.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organism
- Escherichia coli
- Chains
- 56
- Atoms
- 147,155
- Mol. weight
- 2184.5 kDa
- Released
- 14 Dec 2016
Explore 5MGP in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5MGP contains 224 α-helices and 342 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: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-15 | 7 | |
| β-strand | 28-29 | 2 | 107 |
| β-strand | 36-37 | 2 | 107 |
| β-strand | 41 | 1 | 64 |
| β-strand | 47-48 | 2 | 108 |
| β-strand | 51-52 | 2 | 108 |
Chain 1: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-12 | 7 | 1 |
| β-strand | 19-24 | 6 | 1 |
| β-strand | 35-39 | 5 | 1 |
| β-strand | 44-51 | 8 | 1 |
Chain 2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-21 | 4 | |
| 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 | 12 |
| β-strand | 21-23 | 3 | 12 |
| α-helix | 37-42 | 6 | |
| β-strand | 47-48 | 2 | 12 |
| α-helix | 49-50 | 2 | |
| α-helix | 52-54 | 3 | |
| α-helix | 55-60 | 6 | |
Chain 4: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 17 |
| β-strand | 14-19 | 6 | 17 |
| β-strand | 22-27 | 6 | 17 |
| α-helix | 31-33 | 3 | |
| β-strand | 35 | 1 | 17 |
Chain 6: 1 helix, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-16 | 7 | 20 |
| β-strand | 20-26 | 7 | 20 |
| β-strand | 31-33 | 3 | 20 |
| α-helix | 57-64 | 8 | |
Chain b: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-29 | 6 | |
| β-strand | 30-32 | 3 | 30 |
| β-strand | 38-40 | 3 | 30 |
| α-helix | 42-61 | 20 | |
| β-strand | 66-69 | 4 | 31 |
| α-helix | 75-86 | 12 | |
| β-strand | 89-91 | 3 | 31 |
| α-helix | 103-116 | 14 | |
| α-helix | 118-121 | 4 | |
| α-helix | 130-146 | 17 | |
| β-strand | 159-162 | 4 | 31 |
| α-helix | 169-177 | 9 | |
| β-strand | 184-186 | 3 | 31 |
| β-strand | 198-200 | 3 | 31 |
| α-helix | 209-223 | 15 | |
Chain c: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 8-10 | 3 | |
| β-strand | 19-20 | 2 | 36 |
| α-helix | 30-45 | 16 | |
| β-strand | 51-57 | 7 | 36 |
| β-strand | 64-69 | 6 | 36 |
| α-helix | 72-76 | 5 | |
| α-helix | 81-90 | 10 | |
| β-strand | 100-104 | 5 | 36 |
| α-helix | 112-124 | 13 | |
| α-helix | 129-141 | 13 | |
| β-strand | 147-154 | 8 | 37 |
| β-strand | 163-170 | 8 | 37 |
| β-strand | 180-189 | 10 | 37 |
| β-strand | 194-204 | 11 | 37 |
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 ribosomal RNA | A | RNA | 2903 | Escherichia coli | |
| 5S ribosomal RNA | B | RNA | 120 | Escherichia coli | |
| 50S ribosomal protein L2 | C | protein | 271 | Escherichia coli | P60422 (AlphaFold model) |
| 50S ribosomal protein L3 | D | protein | 209 | Escherichia coli | P60438 (AlphaFold model) |
| 50S ribosomal protein L4 | E | protein | 201 | Escherichia coli | P60723 (AlphaFold model) |
| 50S ribosomal protein L5 | F | protein | 177 | Escherichia coli | P62399 (AlphaFold model) |
| 50S ribosomal protein L6 | G | protein | 176 | Escherichia coli | P0AG55 |
| 50S ribosomal protein L9 | H | protein | 149 | Escherichia coli | P0A7R1 |
| 50S ribosomal protein L13 | J | protein | 142 | Escherichia coli | P0AA10 |
| 50S ribosomal protein L14 | K | protein | 122 | Escherichia coli | P0ADY3 |
| 50S ribosomal protein L15 | L | protein | 143 | Escherichia coli | P02413 |
| 50S ribosomal protein L16 | M | protein | 136 | Escherichia coli | P0ADY7 |
44 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>5MGP_1 23S ribosomal RNA (chains A)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUCGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGGAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUAAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCU
Sequence of entity 2 (B), FASTA
>5MGP_2 5S ribosomal RNA (chains B)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAA
Sequence of entity 3 (C), FASTA
>5MGP_3 50S ribosomal protein L2 (chains C)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS
Sequence of entity 4 (D), FASTA
>5MGP_4 50S ribosomal protein L3 (chains D)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 5 (E), FASTA
>5MGP_5 50S ribosomal protein L4 (chains E)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 6 (F), FASTA
>5MGP_6 50S ribosomal protein L5 (chains F)
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAIS
GQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKS
FDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR
Sequence of entity 7 (G), FASTA
>5MGP_7 50S ribosomal protein L6 (chains G)
SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADG
WAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGI
TAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK
Sequence of entity 8 (H), FASTA
>5MGP_8 50S ribosomal protein L9 (chains H)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE
Sequence of entity 9 (J), FASTA
>5MGP_9 50S ribosomal protein L13 (chains J)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI
Sequence of entity 10 (K), FASTA
>5MGP_10 50S ribosomal protein L14 (chains K)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EV
Sequence of entity 11 (L), FASTA
>5MGP_11 50S ribosomal protein L15 (chains L)
RLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRL
PKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVT
VRGLRVTKGARAAIEAAGGKIEE
Sequence of entity 12 (M), FASTA
>5MGP_12 50S ribosomal protein L16 (chains M)
MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQ
GKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLA
AAKLPIKTTFVTKTVM
Primary citation
Structural basis for ArfA-RF2-mediated translation termination on mRNAs lacking stop codons. Huter, P., Muller, C., Beckert, B. et al. Nature (2017) 541:546-549. DOI 10.1038/nature20821 · 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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