4V9O: 50S ribosomal protein L2
Control of ribosomal subunit rotation by elongation factor G. Determined by X-ray diffraction at 2.9 Å resolution. Released 9 Jul 2014.
- Method
- X-ray diffraction
- Resolution
- 2.9 Å
- Organisms
- Escherichia coli, Streptomyces
- Chains
- 220
- Atoms
- 592,086
- Mol. weight
- 8946.54 kDa
- Ligands
- MG, ZN, GCP
- Released
- 9 Jul 2014
Explore 4V9O in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4V9O contains 1,028 α-helices and 1,509 β-strands across 204 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 A0: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| α-helix | 9-15 | 7 | |
| α-helix | 16-18 | 3 | |
| β-strand | 27-29 | 3 | 1 |
| β-strand | 36-38 | 3 | 1 |
| β-strand | 47-48 | 2 | 2 |
| β-strand | 51-52 | 2 | 2 |
Chains A1 and C1: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-12 | 7 | 26 |
| β-strand | 19-24 | 6 | 26 |
| β-strand | 35-39 | 5 | 26 |
| β-strand | 44-49 | 6 | 26 |
Chains A2, C2, E2 and G2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-36 | 12 | |
Chains A3 and G3: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 7-10 | 4 | |
| β-strand | 23 | 1 | 68 |
| α-helix | 37-42 | 6 | |
| β-strand | 47 | 1 | 68 |
| α-helix | 48-50 | 3 | |
| α-helix | 54-60 | 7 | |
Chains A4, C4, E4 and G4: 1 helix, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 83 |
| β-strand | 14 | 1 | 84 |
| β-strand | 17-19 | 3 | 85 |
| β-strand | 22-24 | 3 | 85 |
| β-strand | 25 | 1 | 83 |
| β-strand | 27 | 1 | 84 |
| α-helix | 31-33 | 3 | |
| β-strand | 35 | 1 | 83 |
Chain A5: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| α-helix | 9-18 | 10 | |
| β-strand | 24 | 1 | 101 |
| α-helix | 34-46 | 13 | |
| β-strand | 52 | 1 | 102 |
| α-helix | 60-63 | 4 | |
| β-strand | 86 | 1 | 101 |
| β-strand | 87 | 1 | 102 |
| α-helix | 95-103 | 9 | |
| α-helix | 134-138 | 5 | |
| α-helix | 140-147 | 8 | |
Chain A6: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| α-helix | 16-19 | 4 | |
| α-helix | 25-28 | 4 | |
Chain AC: 8 helices, 29 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 14 |
| β-strand | 16-18 | 3 | 14 |
| α-helix | 30-32 | 3 | |
| β-strand | 33-34 | 2 | 15 |
| β-strand | 42 | 1 | 16 |
| β-strand | 48 | 1 | 16 |
| β-strand | 53 | 1 | 17 |
| α-helix | 60 | 1 | |
| β-strand | 61-62 | 2 | 15 |
| β-strand | 71 | 1 | 18 |
| β-strand | 74-75 | 2 | 19 |
| β-strand | 79-81 | 3 | 20 |
| β-strand | 90-92 | 3 | 20 |
| β-strand | 95 | 1 | 19 |
| β-strand | 102-103 | 2 | 20 |
| β-strand | 106 | 1 | 21 |
| β-strand | 115-116 | 2 | 19 |
| β-strand | 117 | 1 | 18 |
| β-strand | 128 | 1 | 22 |
| α-helix | 131-133 | 3 | |
| β-strand | 143 | 1 | 23 |
| β-strand | 153 | 1 | 23 |
| β-strand | 162-165 | 4 | 24 |
| β-strand | 171-174 | 4 | 24 |
| β-strand | 180-183 | 4 | 24 |
| β-strand | 189 | 1 | 23 |
| β-strand | 190 | 1 | 22 |
| β-strand | 194 | 1 | 21 |
| α-helix | 198-201 | 4 | |
| α-helix | 207-211 | 5 | |
| β-strand | 215 | 1 | 17 |
| α-helix | 216-218 | 3 | |
| α-helix | 221-223 | 3 | |
| β-strand | 244 | 1 | 25 |
| β-strand | 250 | 1 | 25 |
| α-helix | 263-265 | 3 | |
| β-strand | 266-268 | 3 | 24 |
159 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 |
|---|
| 5S rRNA | AB, CB, EB, GB | RNA | 120 | Escherichia coli | |
| 50S ribosomal protein L2 | AC, CC, EC, GC | protein | 273 | Escherichia coli | P60422 (AlphaFold model) |
| 23S rRNA | AA, CA, EA, GA | RNA | 2904 | Escherichia coli | |
| 50S ribosomal protein L3 | AD, CD, ED, GD | protein | 209 | Escherichia coli | P60438 (AlphaFold model) |
| 50S ribosomal protein L4 | AE, CE, EE, GE | protein | 201 | Escherichia coli | P60723 (AlphaFold model) |
| 50S ribosomal protein L5 | AF, CF, EF, GF | protein | 179 | Escherichia coli | P62399 (AlphaFold model) |
| 50S ribosomal protein L6 | AG, CG, EG, GG | protein | 177 | Escherichia coli | P0AG55 |
| 50S ribosomal protein L9 | AH, CH, EH, GH | protein | 50 | Escherichia coli | P0A7R1 |
| 50S ribosomal protein L11 | AI, CI, EI, GI | protein | 142 | Escherichia coli | P0A7J7 |
| 50S ribosomal protein L13 | AJ, CJ, EJ, GJ | protein | 142 | Escherichia coli | P0AA10 |
| 50S ribosomal protein L14 | AK, CK, EK, GK | protein | 123 | Escherichia coli | P0ADY3 |
| 50S ribosomal protein L15 | AL, CL, EL, GL | protein | 144 | Escherichia coli | P02413 |
44 more molecules are not listed.
Sequence of entity 1 (AB, CB, EB, GB), FASTA
>4V9O_1 5S rRNA (chains AB, CB, EB, GB)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU
Sequence of entity 2 (AC, CC, EC, GC), FASTA
>4V9O_2 50S ribosomal protein L2 (chains AC, CC, EC, GC)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK
Sequence of entity 3 (AA, CA, EA, GA), FASTA
>4V9O_3 23S rRNA (chains AA, CA, EA, GA)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
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 4 (AD, CD, ED, GD), FASTA
>4V9O_4 50S ribosomal protein L3 (chains AD, CD, ED, GD)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 5 (AE, CE, EE, GE), FASTA
>4V9O_5 50S ribosomal protein L4 (chains AE, CE, EE, GE)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 6 (AF, CF, EF, GF), FASTA
>4V9O_6 50S ribosomal protein L5 (chains AF, CF, EF, GF)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK
Sequence of entity 7 (AG, CG, EG, GG), FASTA
>4V9O_7 50S ribosomal protein L6 (chains AG, CG, EG, GG)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK
Sequence of entity 8 (AH, CH, EH, GH), FASTA
>4V9O_8 50S ribosomal protein L9 (chains AH, CH, EH, GH)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEAR
Sequence of entity 9 (AI, CI, EI, GI), FASTA
>4V9O_9 50S ribosomal protein L11 (chains AI, CI, EI, GI)
MAKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVIT
VYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGA
DIEAMTRSIEGTARSMGLVVED
Sequence of entity 10 (AJ, CJ, EJ, GJ), FASTA
>4V9O_10 50S ribosomal protein L13 (chains AJ, CJ, EJ, GJ)
MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD
KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFR
KLKVYAGNEHNHAAQQPQVLDI
Sequence of entity 11 (AK, CK, EK, GK), FASTA
>4V9O_11 50S ribosomal protein L14 (chains AK, CK, EK, GK)
MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKA
VVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAP
EVL
Sequence of entity 12 (AL, CL, EL, GL), FASTA
>4V9O_12 50S ribosomal protein L15 (chains AL, CL, EL, GL)
MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRR
LPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPV
TVRGLRVTKGARAAIEAAGGKIEE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 748 |
| ZN | Zinc ion | Zn | 4 |
| GCP | Phosphomethylphosphonic acid guanylate ester | C11 H18 N5 O13 P3 | 4 |
Primary citation
Control of ribosomal subunit rotation by elongation factor G. Pulk, A., Cate, J.H. Science (2013) 340:1235970-1235970. DOI 10.1126/science.1235970 · 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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