6C4I: 50S ribosomal protein L2
Conformation of methylated GGQ in the peptidyl transferase center during translation termination. Determined by electron microscopy at 3.24 Å resolution. Released 21 Feb 2018.
- Method
- Electron microscopy
- Resolution
- 3.24 Å
- Organism
- Escherichia coli
- Chains
- 59
- Atoms
- 151,446
- Mol. weight
- 2282.07 kDa
- Ligands
- MG, ZN
- Released
- 21 Feb 2018
Explore 6C4I in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6C4I contains 285 α-helices and 332 β-strands across 53 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 | 4-9 | 6 | 1 |
| α-helix | 18-27 | 10 | |
| β-strand | 35-39 | 5 | 1 |
| α-helix | 42-50 | 9 | |
| β-strand | 55-58 | 4 | 1 |
Chain 1: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-8 | 2 | |
| β-strand | 10-15 | 6 | 2 |
| β-strand | 22-26 | 5 | 2 |
| α-helix | 31 | 1 | |
| β-strand | 32-33 | 2 | 2 |
| α-helix | 46-51 | 6 | |
| α-helix | 56-64 | 9 | |
Chain 2: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| α-helix | 10-16 | 7 | |
| α-helix | 17-19 | 3 | |
| α-helix | 21-25 | 5 | |
| β-strand | 29-30 | 2 | 12 |
| α-helix | 31 | 1 | |
| β-strand | 37-38 | 2 | 12 |
| β-strand | 42 | 1 | 62 |
| β-strand | 48-49 | 2 | 13 |
| β-strand | 52-53 | 2 | 13 |
Chain 3: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-13 | 7 | 19 |
| β-strand | 20-25 | 6 | 19 |
| α-helix | 33-34 | 2 | |
| β-strand | 35-40 | 6 | 19 |
| β-strand | 45-53 | 9 | 19 |
Chain 4: 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 5: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 8-13 | 6 | |
| β-strand | 15-16 | 2 | 24 |
| β-strand | 22-24 | 3 | 24 |
| α-helix | 25-26 | 2 | |
| α-helix | 38-44 | 7 | |
| β-strand | 48-49 | 2 | 24 |
| α-helix | 50-51 | 2 | |
| α-helix | 52-61 | 10 | |
Chain 6: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 29 |
| β-strand | 14-18 | 5 | 29 |
| β-strand | 23-27 | 5 | 29 |
| α-helix | 31-33 | 3 | |
| β-strand | 35-37 | 3 | 29 |
Chain b: 13 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-12 | 7 | |
| β-strand | 16-19 | 4 | 34 |
| α-helix | 20-22 | 3 | |
| α-helix | 25-27 | 3 | |
| β-strand | 31-35 | 5 | 34 |
| β-strand | 38-41 | 4 | 34 |
| α-helix | 43-62 | 20 | |
| β-strand | 67-70 | 4 | 35 |
| α-helix | 74-86 | 13 | |
| β-strand | 90-92 | 3 | 35 |
| α-helix | 96-97 | 2 | |
| α-helix | 104-119 | 16 | |
| α-helix | 120-124 | 5 | |
| α-helix | 131-148 | 18 | |
| α-helix | 151-153 | 3 | |
| β-strand | 160-163 | 4 | 35 |
| α-helix | 170-179 | 10 | |
| α-helix | 181-182 | 2 | |
| β-strand | 183-187 | 5 | 35 |
| β-strand | 198-201 | 4 | 35 |
| α-helix | 207-226 | 20 | |
45 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 | 120 | Escherichia coli | |
| 50S ribosomal protein L2 | C | protein | 273 | 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 | 177 | Escherichia coli | P0AG55 |
| 50S ribosomal protein L9 | H | protein | 149 | Escherichia coli | P0A7R1 |
| 50S ribosomal protein L10 | I | protein | 165 | Escherichia coli | P0A7J3 |
| 50S ribosomal protein L11 | J | protein | 142 | Escherichia coli | P0A7J7 |
| 50S ribosomal protein L13 | K | protein | 142 | Escherichia coli | P0AA10 |
| 50S ribosomal protein L14 | L | protein | 123 | Escherichia coli | P0ADY3 |
46 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6C4I_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
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACXAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCUU
Sequence of entity 2 (B), FASTA
>6C4I_2 5S rRNA (chains B)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU
Sequence of entity 3 (C), FASTA
>6C4I_3 50S ribosomal protein L2 (chains C)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK
Sequence of entity 4 (D), FASTA
>6C4I_4 50S ribosomal protein L3 (chains D)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 5 (E), FASTA
>6C4I_5 50S ribosomal protein L4 (chains E)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 6 (F), FASTA
>6C4I_6 50S ribosomal protein L5 (chains F)
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAIS
GQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKS
FDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR
Sequence of entity 7 (G), FASTA
>6C4I_7 50S ribosomal protein L6 (chains G)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK
Sequence of entity 8 (H), FASTA
>6C4I_8 50S ribosomal protein L9 (chains H)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE
Sequence of entity 9 (I), FASTA
>6C4I_9 50S ribosomal protein L10 (chains I)
MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLL
RRAVEGTPFECLKDAFVGPTLIAYSMEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPA
SQIDRLATLPTYEEAIARLMATMKEASAGKLVRTLAAVRDAKEAA
Sequence of entity 10 (J), FASTA
>6C4I_10 50S ribosomal protein L11 (chains J)
MAKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVIT
VYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGA
DIEAMTRSIEGTARSMGLVVED
Sequence of entity 11 (K), FASTA
>6C4I_11 50S ribosomal protein L13 (chains K)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI
Sequence of entity 12 (L), FASTA
>6C4I_12 50S ribosomal protein L14 (chains L)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EVL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 317 |
| ZN | Zinc ion | Zn | 2 |
Primary citation
Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination. Zeng, F., Jin, H. Sci Rep (2018) 8:2349-2349. DOI 10.1038/s41598-018-20107-8 · 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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