6WNT: 50S ribosomal protein L2
50S ribosomal subunit without free 5S rRNA and perturbed PTC. Determined by electron microscopy at 3.1 Å resolution. Released 24 Jun 2020.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organism
- Escherichia coli
- Chains
- 31
- Atoms
- 91,164
- Mol. weight
- 1379.39 kDa
- Released
- 24 Jun 2020
Explore 6WNT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6WNT contains 122 α-helices and 210 β-strands across 30 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 a: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-11 | 6 | |
| β-strand | 21 | 1 | 22 |
| α-helix | 23-33 | 11 | |
| β-strand | 41-47 | 7 | 22 |
| α-helix | 48 | 1 | |
| β-strand | 60-64 | 5 | 23 |
| β-strand | 160-164 | 5 | 23 |
| β-strand | 170-177 | 8 | 22 |
| α-helix | 182-197 | 16 | |
| β-strand | 211-216 | 6 | 22 |
| β-strand | 221 | 1 | 22 |
| β-strand | 224 | 1 | 22 |
Chain A: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| β-strand | 10-14 | 5 | 67 |
| β-strand | 15 | 1 | 68 |
| β-strand | 22-26 | 5 | 67 |
| β-strand | 33 | 1 | 68 |
Chain b: 4 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 1 |
| β-strand | 16-18 | 3 | 1 |
| α-helix | 30-32 | 3 | |
| β-strand | 33-35 | 3 | 2 |
| β-strand | 42 | 1 | 3 |
| β-strand | 48 | 1 | 3 |
| β-strand | 53 | 1 | 4 |
| β-strand | 60-62 | 3 | 2 |
| β-strand | 71 | 1 | 5 |
| β-strand | 74-81 | 8 | 6 |
| β-strand | 90-95 | 6 | 6 |
| β-strand | 99-104 | 6 | 6 |
| β-strand | 106 | 1 | 7 |
| β-strand | 114-116 | 3 | 6 |
| β-strand | 117 | 1 | 5 |
| β-strand | 128-130 | 3 | 8 |
| α-helix | 131-133 | 3 | |
| β-strand | 139-141 | 3 | 8 |
| β-strand | 143 | 1 | 9 |
| β-strand | 153 | 1 | 9 |
| β-strand | 161-165 | 5 | 8 |
| β-strand | 170-174 | 5 | 8 |
| β-strand | 180-184 | 5 | 8 |
| β-strand | 188-191 | 4 | 8 |
| β-strand | 194 | 1 | 7 |
| β-strand | 203 | 1 | 1 |
| α-helix | 207-211 | 5 | |
| β-strand | 215 | 1 | 4 |
| α-helix | 216-217 | 2 | |
| β-strand | 244 | 1 | 10 |
| β-strand | 250 | 1 | 10 |
| β-strand | 266-268 | 3 | 8 |
Chain B: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-15 | 7 | |
| β-strand | 28-29 | 2 | 69 |
| α-helix | 30 | 1 | |
| β-strand | 36-37 | 2 | 69 |
| β-strand | 41 | 1 | 44 |
| β-strand | 48 | 1 | 70 |
| β-strand | 51 | 1 | 70 |
Chain c: 4 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-5 | 2 | 11 |
| β-strand | 7-15 | 9 | 12 |
| β-strand | 21-28 | 8 | 12 |
| β-strand | 32-33 | 2 | 13 |
| β-strand | 36-38 | 3 | 14 |
| β-strand | 47-50 | 4 | 14 |
| α-helix | 62-71 | 10 | |
| β-strand | 80-83 | 4 | 14 |
| β-strand | 95-96 | 2 | 13 |
| α-helix | 98-103 | 6 | |
| β-strand | 106-112 | 7 | 11 |
| β-strand | 115-119 | 5 | 15 |
| α-helix | 121-125 | 5 | |
| α-helix | 127-130 | 4 | |
| β-strand | 163-166 | 4 | 15 |
| β-strand | 169-176 | 8 | 11 |
| β-strand | 177-181 | 5 | 12 |
| β-strand | 186-190 | 5 | 12 |
| β-strand | 202-205 | 4 | 11 |
Chain d: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 17 |
| β-strand | 11-13 | 3 | 17 |
| α-helix | 16-19 | 4 | |
| α-helix | 25-37 | 13 | |
| α-helix | 98-114 | 17 | |
| β-strand | 118-121 | 4 | 18 |
| α-helix | 131-138 | 8 | |
| β-strand | 146-150 | 5 | 18 |
| α-helix | 155-160 | 6 | |
| β-strand | 168-171 | 4 | 18 |
| α-helix | 172-174 | 3 | |
| α-helix | 177-182 | 6 | |
| β-strand | 185-189 | 5 | 18 |
| α-helix | 190-199 | 10 | |
Chain D: 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 e: 10 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-6 | 5 | |
| α-helix | 7-11 | 5 | |
| α-helix | 12-18 | 7 | |
| β-strand | 32-37 | 6 | 20 |
| α-helix | 41-43 | 3 | |
| α-helix | 46-59 | 14 | |
| β-strand | 65-67 | 3 | 20 |
| β-strand | 73 | 1 | 21 |
| β-strand | 78 | 1 | 21 |
| β-strand | 85-87 | 3 | 20 |
| β-strand | 90 | 1 | 20 |
| α-helix | 93-101 | 9 | |
| α-helix | 102-106 | 5 | |
| α-helix | 107-109 | 3 | |
| β-strand | 121 | 1 | 20 |
| β-strand | 127-129 | 3 | 20 |
| β-strand | 152-156 | 5 | 20 |
| α-helix | 162-169 | 8 | |
| α-helix | 170-172 | 3 | |
22 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 |
|---|
| 50S ribosomal protein L2 | b | protein | 271 | Escherichia coli | P60422 (AlphaFold model) |
| 50S ribosomal protein L3 | c | protein | 209 | Escherichia coli | P60438 (AlphaFold model) |
| 50S ribosomal protein L4 | d | protein | 201 | Escherichia coli | P60723 (AlphaFold model) |
| 50S ribosomal protein L5 | e | protein | 177 | Escherichia coli | P62399 (AlphaFold model) |
| 50S ribosomal protein L6 | f | protein | 176 | Escherichia coli | P0AG55 |
| 50S ribosomal protein L9 | g | protein | 149 | Escherichia coli | P0A7R1 |
| 50S ribosomal protein L10 | h | protein | 131 | Escherichia coli | P0A7J3 |
| 50S ribosomal protein L11 | i | protein | 141 | Escherichia coli | P0A7J7 |
| 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 L17 | n | protein | 120 | Escherichia coli | P0AG44 |
19 more molecules are not listed.
Sequence of entity 1 (b), FASTA
>6WNT_1 50S ribosomal protein L2 (chains b)
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQA
YRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVD
AAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEM
RKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFG
KHPVTPWGVQTKGKKTRSNKRTDKFIVRRRS
Sequence of entity 2 (c), FASTA
>6WNT_2 50S ribosomal protein L3 (chains c)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 3 (d), FASTA
>6WNT_3 50S ribosomal protein L4 (chains d)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 4 (e), FASTA
>6WNT_4 50S ribosomal protein L5 (chains e)
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAIS
GQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKS
FDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR
Sequence of entity 5 (f), FASTA
>6WNT_5 50S ribosomal protein L6 (chains f)
SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADG
WAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGI
TAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK
Sequence of entity 6 (g), FASTA
>6WNT_6 50S ribosomal protein L9 (chains g)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE
Sequence of entity 7 (h), FASTA
>6WNT_7 50S ribosomal protein L10 (chains h)
MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLL
RRAVEGTPFECLKDAFVGPTLIAYSMEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPA
SQIDRLATLPT
Sequence of entity 8 (i), FASTA
>6WNT_8 50S ribosomal protein L11 (chains i)
AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITV
YADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGAD
IEAMTRSIEGTARSMGLVVED
Sequence of entity 9 (j), FASTA
>6WNT_9 50S ribosomal protein L13 (chains j)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI
Sequence of entity 10 (k), FASTA
>6WNT_10 50S ribosomal protein L14 (chains k)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EV
Sequence of entity 11 (l), FASTA
>6WNT_11 50S ribosomal protein L15 (chains l)
RLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRL
PKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVT
VRGLRVTKGARAAIEAAGGKIEE
Sequence of entity 12 (n), FASTA
>6WNT_12 50S ribosomal protein L17 (chains n)
MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSV
ANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSE
Primary citation
Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly. Huang, S., Aleksashin, N.A., Loveland, A.B. et al. Nat Commun (2020) 11:2900-2900. DOI 10.1038/s41467-020-16694-8 · 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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