4Y4O: 50S ribosomal protein L2
Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and bound to protein Y (YfiA) at 2.3A resolution. Determined by X-ray diffraction at 2.3 Å resolution. Released 18 Mar 2015.
- Method
- X-ray diffraction
- Resolution
- 2.3 Å
- Organisms
- Thermus thermophilus HB8, Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), Escherichia coli (strain K12)
- Chains
- 106
- Atoms
- 298,502
- Mol. weight
- 4426.44 kDa
- Ligands
- MG, ARG, ZN, SF4
- Released
- 18 Mar 2015
Explore 4Y4O in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4Y4O contains 524 α-helices and 659 β-strands across 100 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.
Chains 10 and 20: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| β-strand | 22-23 | 2 | 184 |
| β-strand | 30-31 | 2 | 185 |
| β-strand | 36-39 | 4 | 184 |
| β-strand | 46-47 | 2 | 185 |
| β-strand | 51-53 | 3 | 184 |
| β-strand | 59-61 | 3 | 184 |
| β-strand | 65-71 | 7 | 185 |
| α-helix | 73-75 | 3 | |
| β-strand | 77-83 | 7 | 185 |
Chains 11 and 21: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-21 | 9 | 192 |
| α-helix | 25-27 | 3 | |
| β-strand | 33-42 | 10 | 192 |
| β-strand | 46-53 | 8 | 193 |
| β-strand | 56-63 | 8 | 193 |
| α-helix | 64-66 | 3 | |
| α-helix | 67-76 | 10 | |
| α-helix | 77-79 | 3 | |
| α-helix | 87-96 | 10 | |
Chains 12 and 22: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| α-helix | 18-40 | 23 | |
| α-helix | 48-69 | 22 | |
Chain 13: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-8 | 6 | 203 |
| α-helix | 17-25 | 9 | |
| β-strand | 34-38 | 5 | 203 |
| α-helix | 41-49 | 9 | |
| β-strand | 54-59 | 6 | 203 |
Chain 14: 1 helix, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-9 | 3 | |
| β-strand | 10-16 | 7 | 206 |
| β-strand | 21-26 | 6 | 206 |
| β-strand | 30-33 | 4 | 206 |
Chain 15: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-12 | 3 | |
| α-helix | 13-19 | 7 | |
| α-helix | 20-22 | 3 | |
| α-helix | 24-29 | 6 | |
| β-strand | 31-32 | 2 | 1 |
| β-strand | 39-40 | 2 | 1 |
| β-strand | 45 | 1 | 119 |
| β-strand | 51-52 | 2 | 2 |
| β-strand | 55-56 | 2 | 2 |
Chains 16 and 26: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-13 | 8 | 6 |
| β-strand | 19-26 | 8 | 6 |
| α-helix | 33-34 | 2 | |
| β-strand | 35-40 | 6 | 6 |
| β-strand | 45-53 | 9 | 6 |
Chains 17 and 27: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-37 | 13 | |
77 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 | 1A, 2A | RNA | 2915 | Thermus thermophilus HB8 | |
| 5S Ribosomal RNA | 1B, 2B | RNA | 121 | Thermus thermophilus HB8 | |
| 50S ribosomal protein L2 | 1D, 2D | protein | 276 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P60405 (AlphaFold model) |
| 50S ribosomal protein L3 | 1E, 2E | protein | 206 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHN8 (AlphaFold model) |
| 50S ribosomal protein L4 | 1F, 2F | protein | 210 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHN9 (AlphaFold model) |
| 50S ribosomal protein L5 | 1G, 2G | protein | 182 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHQ0 (AlphaFold model) |
| 50S ribosomal protein L6 | 1H, 2H | protein | 180 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P0DOY8 |
| 50S ribosomal protein L9 | 1I, 2I | protein | 148 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SLQ1 |
| 50S ribosomal protein L13 | 1N, 2N | protein | 140 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P60488 |
| 50S ribosomal protein L14 | 1O, 2O | protein | 122 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHP8 |
| 50S ribosomal protein L15 | 1P, 2P | protein | 150 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHQ7 |
| 50S ribosomal protein L16 | 1Q, 2Q | protein | 141 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P60489 |
41 more molecules are not listed.
Sequence of entity 1 (1A, 2A), FASTA
>4Y4O_1 23S Ribosomal RNA (chains 1A, 2A)
GUCAAGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGC
UACCUGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGG
GGAACCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUGCGCGGGGGGAACCUGGGGAAC
UGAAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAG
CGAAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGAC
ACCGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCC
GUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCA
UGGGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCAC
CAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAAC
CGUGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGA
GCCGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCG
AGUCCGAACAGGGCGCAAGCGGGCCGCACGCGGCCCGCAAAGUCCGCGGCCGUGGACCCG
AAACCGGGCGAGCUAGCCCUGGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGA
ACCGGUGGGGGAUGCAAACCCCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAG
CCCGGAGAUAGCUGGUUCUCCCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGG
GCCUGUAGAGCACUGAUAGGGCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCC
GAAGGGUCCCAGGUGGAGCCUGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCG
CGGGAACAACCGAGACCGCCAGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGU
GGCGCCGCGAAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUA
AUAGCUCACUGGUCGAGUGGCGCCGCGCCGAAAAUGAUCGGGGCUUAAGCCCAGCGCCGA
AGCUGCGGGUCUGGGGGAUGACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGG
CCGACCCGCGAGGGCGGCUGGAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAA
AGAGGGUGAGAAUCCCUCUCGCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGU
AGGGUUAGGCGGGACCUAAGGUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUA
UUCCGGCCCUUCCCGCAGGUGCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAU
GGACGAGCCCGGCCAGAAGCGCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAACAAGCUC
UGCGUGGUGGGGAAGCCCGUACGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGC
CUCUAAGCACAACCUGCGGGAACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGA
GCACUCAGGCGCGCGGGAGAACCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUC
GGGAGAAGGGGUGCUCCCUGGGGUGAUGAGCCCCGGGGAGCCGCAGUGAACAGGCUCUGG
CGACUGUUUACCAAAAACACAGCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGAC
GCUUGCCCGGUGCCGGAAGGUCAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUG
AACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCG
ACCUGCACGAAAAGCGUAACGACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGA
ACUGGCCGUGAAGAUGCGGCCUACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACU
GCAGCCUGGUGUUGGCUCUUGGUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCC
CGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAA
CCCUCGGAUGGGGGGACAGCGCUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAA
GGUAACGGAGGCGCCCAAAGGUCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAG
GGUAGAAGGGGGCCUGACUGCGAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAG
UGAACCGGUGGUCCCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAU
AACAGGCUGAUCUCCCCCGAGCGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGG
CUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCG
GCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCA
GGAGGCUUGAGGGGGGCUCUUCCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUU
CCCAGCUGUCCCUCCAGGGGCAUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGA
AAGCAUCUAAGCGGGAAGCCCGCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAG
GACCCGGGAAGACCACCCGGUGGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCC
GACCGGUCCCAAUCGUCCGAGGUCUUGACCCCUCC
Sequence of entity 2 (1B, 2B), FASTA
>4Y4O_2 5S Ribosomal RNA (chains 1B, 2B)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
U
Sequence of entity 3 (1D, 2D), FASTA
>4Y4O_3 50S ribosomal protein L2 (chains 1D, 2D)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK
Sequence of entity 4 (1E, 2E), FASTA
>4Y4O_4 50S ribosomal protein L3 (chains 1E, 2E)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK
Sequence of entity 5 (1F, 2F), FASTA
>4Y4O_5 50S ribosomal protein L4 (chains 1F, 2F)
MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS
GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE
GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG
LNVYDIVRTERLVMDLDAWEVFQNRIGGEA
Sequence of entity 6 (1G, 2G), FASTA
>4Y4O_6 50S ribosomal protein L5 (chains 1G, 2G)
MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK
Sequence of entity 7 (1H, 2H), FASTA
>4Y4O_7 50S ribosomal protein L6 (chains 1H, 2H)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK
Sequence of entity 8 (1I, 2I), FASTA
>4Y4O_8 50S ribosomal protein L9 (chains 1I, 2I)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE
Sequence of entity 9 (1N, 2N), FASTA
>4Y4O_9 50S ribosomal protein L13 (chains 1N, 2N)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV
Sequence of entity 10 (1O, 2O), FASTA
>4Y4O_10 50S ribosomal protein L14 (chains 1O, 2O)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL
Sequence of entity 11 (1P, 2P), FASTA
>4Y4O_11 50S ribosomal protein L15 (chains 1P, 2P)
MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLM
RLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAGLLKKGYRLKILGEGEA
KPLKVVAHAFSKSALEKLKAAGGEPVLLEA
Sequence of entity 12 (1Q, 2Q), FASTA
>4Y4O_12 50S ribosomal protein L16 (chains 1Q, 2Q)
MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAARVAMVRHFRR
GGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPGRVMFEVAGVTEEQAMEALRI
AGHKLPIKTKIVRRDAYDEAQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 2517 |
| ARG | Arginine | C6 H15 N4 O2 | 2 |
| ZN | Zinc ion | Zn | 12 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
Water and common crystallization additives (MPD) are not listed.
Primary citation
Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Polikanov, Y.S., Melnikov, S.V., Soll, D. et al. Nat Struct Mol Biol (2015) 22:342-344. DOI 10.1038/nsmb.2992 · PubMed
Other PDB entries of the same protein (UniProt P60405 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9NO7 2.13 Å, Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 8CVL 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
- 8FC6 2.35 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
- 8VTW 2.35 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 4W2F 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin,…
- 6XHV 2.4 Å, Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex…
- 7RQA 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
- 7RQE 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
- 8CVJ 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
- 8VTU 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 8VTX 2.4 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
- 9MTP 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
Browse structure collections
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