6I0Y: 50S ribosomal protein L24
TnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel. Determined by electron microscopy at 3.2 Å resolution. Released 5 Dec 2018.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organisms
- Escherichia coli, Homo sapiens
- Chains
- 36
- Atoms
- 93,619
- Mol. weight
- 1414.24 kDa
- Ligands
- MG, ZN, TRP
- Released
- 5 Dec 2018
Explore 6I0Y in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6I0Y contains 137 α-helices and 229 β-strands across 33 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: 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 | 7 |
| β-strand | 36-38 | 3 | 7 |
| β-strand | 47-48 | 2 | 8 |
| β-strand | 51-52 | 2 | 8 |
Chain 1: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-12 | 7 | 14 |
| β-strand | 19-24 | 6 | 14 |
| β-strand | 35-39 | 5 | 14 |
| β-strand | 44-49 | 6 | 14 |
Chain 2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-36 | 12 | |
Chain 3: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 7-10 | 4 | |
| β-strand | 23 | 1 | 21 |
| α-helix | 37-42 | 6 | |
| β-strand | 47 | 1 | 21 |
| α-helix | 48-50 | 3 | |
| α-helix | 54-60 | 7 | |
Chain 4: 1 helix, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 22 |
| β-strand | 14 | 1 | 23 |
| β-strand | 17-19 | 3 | 24 |
| β-strand | 22-24 | 3 | 24 |
| β-strand | 25 | 1 | 22 |
| β-strand | 27 | 1 | 23 |
| α-helix | 31-33 | 3 | |
| β-strand | 35 | 1 | 22 |
Chain 5: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| α-helix | 9-18 | 10 | |
| β-strand | 24 | 1 | 27 |
| α-helix | 34-46 | 13 | |
| β-strand | 52 | 1 | 28 |
| α-helix | 60-63 | 4 | |
| β-strand | 86 | 1 | 27 |
| β-strand | 87 | 1 | 28 |
| α-helix | 95-103 | 9 | |
| α-helix | 134-138 | 5 | |
| α-helix | 140-147 | 8 | |
Chain 6: 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 7: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-15 | 4 | |
| α-helix | 17-21 | 5 | |
25 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 L24 | h | protein | 104 | Escherichia coli | P60624 (AlphaFold model) |
| 50S ribosomal protein L32 | 0 | protein | 57 | Escherichia coli | P0A7N4 (AlphaFold model) |
| 50S ribosomal protein L33 | 1 | protein | 55 | Escherichia coli | P0A7N9 (AlphaFold model) |
| 50S ribosomal protein L34 | 2 | protein | 46 | Escherichia coli | P0A7P5 (AlphaFold model) |
| 50S ribosomal protein L35 | 3 | protein | 65 | Escherichia coli | P0A7Q1 |
| 50S ribosomal protein L36 | 4 | protein | 38 | Escherichia coli | P0A7Q6 |
| 50S ribosomal protein L10 | 5 | protein | 165 | Escherichia coli | P0A7J3 |
| 50S ribosomal protein L7/L12 | 6 | protein | 121 | Escherichia coli | P0A7K2 |
| Tryptophanase operon leader peptide | 7 | protein | 24 | Escherichia coli | P0AD89 |
| 50S ribosomal protein L25 | 8 | protein | 94 | Escherichia coli | P68919 |
| 23S ribosomal RNA | A | RNA | 2903 | Escherichia coli | |
| 5S ribosomal RNA | B | RNA | 118 | Escherichia coli | |
24 more molecules are not listed.
Sequence of entity 1 (h), FASTA
>6I0Y_1 50S ribosomal protein L24 (chains h)
MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVE
KEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETIK
Sequence of entity 2 (0), FASTA
>6I0Y_2 50S ribosomal protein L32 (chains 0)
MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK
Sequence of entity 3 (1), FASTA
>6I0Y_3 50S ribosomal protein L33 (chains 1)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK
Sequence of entity 4 (2), FASTA
>6I0Y_4 50S ribosomal protein L34 (chains 2)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK
Sequence of entity 5 (3), FASTA
>6I0Y_5 50S ribosomal protein L35 (chains 3)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA
Sequence of entity 6 (4), FASTA
>6I0Y_6 50S ribosomal protein L36 (chains 4)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG
Sequence of entity 7 (5), FASTA
>6I0Y_7 50S ribosomal protein L10 (chains 5)
MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLL
RRAVEGTPFECLKDAFVGPTLIAYSMEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPA
SQIDRLATLPTYEEAIARLMATMKEASAGKLVRTLAAVRDAKEAA
Sequence of entity 8 (6), FASTA
>6I0Y_8 50S ribosomal protein L7/L12 (chains 6)
MSITKDQIIEAVAAMSVMDVVELISAMEEKFGVSAAAAVAVAAGPVEAAEEKTEFDVILK
AAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAGAEVEV
K
Sequence of entity 9 (7), FASTA
>6I0Y_9 Tryptophanase operon leader peptide (chains 7)
MNILHICVTSKWFNIDNKIVDHRP
Sequence of entity 10 (8), FASTA
>6I0Y_10 50S ribosomal protein L25 (chains 8)
MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEV
LTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA
Sequence of entity 11 (A), FASTA
>6I0Y_11 23S ribosomal RNA (chains A)
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
UAAUGAACCGUGAGGCUUAACCU
Sequence of entity 12 (B), FASTA
>6I0Y_12 5S ribosomal RNA (chains B)
GCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACG
CCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 143 |
| ZN | Zinc ion | Zn | 1 |
| TRP | Tryptophan | C11 H12 N2 O2 | 1 |
Primary citation
Folding pathway of an Ig domain is conserved on and off the ribosome. Tian, P., Steward, A., Kudva, R. et al. Proc Natl Acad Sci U S A (2018) 115:E11284-E11293. DOI 10.1073/pnas.1810523115 · PubMed
Other PDB entries of the same protein (UniProt P60624 (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
- 9D89 1.95 Å, E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)
Browse structure collections
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