9IOT: Large ribosomal subunit protein uL29
Cryo-EM structure of Escherichia coli hibernating ribosome with RNase I mutant. Determined by electron microscopy at 2.7 Å resolution. Released 30 Jul 2025.
- Method
- Electron microscopy
- Resolution
- 2.7 Å
- Organism
- Escherichia coli
- Chains
- 56
- Atoms
- 143,360
- Mol. weight
- 2244.63 kDa
- Ligands
- CA, MG
- Released
- 30 Jul 2025
Explore 9IOT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9IOT contains 268 α-helices and 333 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: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| α-helix | 11-33 | 23 | |
| α-helix | 41-61 | 21 | |
Chain 1: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 3 |
| α-helix | 18-26 | 9 | |
| β-strand | 35-39 | 5 | 3 |
| α-helix | 42-50 | 9 | |
| β-strand | 55-58 | 4 | 3 |
Chain 2: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-8 | 2 | |
| β-strand | 10-11 | 2 | 15 |
| β-strand | 14-15 | 2 | 16 |
| β-strand | 21-22 | 2 | 16 |
| β-strand | 25-26 | 2 | 15 |
| β-strand | 32-33 | 2 | 16 |
| α-helix | 42-45 | 4 | |
| α-helix | 56-63 | 8 | |
Chain 3: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-16 | 7 | |
| α-helix | 17-19 | 3 | |
| β-strand | 29-30 | 2 | 6 |
| β-strand | 37-38 | 2 | 6 |
| β-strand | 42 | 1 | 7 |
| β-strand | 48-49 | 2 | 8 |
| β-strand | 52-53 | 2 | 8 |
Chain 4: 0 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-13 | 7 | 13 |
| β-strand | 20-25 | 6 | 13 |
| β-strand | 37-40 | 4 | 14 |
| β-strand | 45-48 | 4 | 14 |
| β-strand | 49-53 | 5 | 13 |
Chain 5: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-21 | 4 | |
| α-helix | 25-37 | 13 | |
Chain 6: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 10-12 | 3 | |
| β-strand | 15-16 | 2 | 20 |
| β-strand | 22-24 | 3 | 20 |
| α-helix | 25-26 | 2 | |
| α-helix | 38-43 | 6 | |
| β-strand | 48-49 | 2 | 20 |
| α-helix | 55-61 | 7 | |
Chain 7: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 21 |
| β-strand | 14-19 | 6 | 21 |
| β-strand | 22-27 | 6 | 21 |
| α-helix | 31-33 | 3 | |
| β-strand | 35-37 | 3 | 21 |
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 |
|---|
| Large ribosomal subunit protein uL29 | 0 | protein | 63 | Escherichia coli | P0A7M6 (AlphaFold model) |
| Large ribosomal subunit protein uL30 | 1 | protein | 59 | Escherichia coli | P0AG51 (AlphaFold model) |
| Large ribosomal subunit protein bL32 | 3 | protein | 57 | Escherichia coli | P0A7N4 (AlphaFold model) |
| Large ribosomal subunit protein bL33 | 4 | protein | 55 | Escherichia coli | P0A7N9 (AlphaFold model) |
| 50S ribosomal protein L34 | 5 | protein | 46 | Escherichia coli | P0A7P5 |
| Large ribosomal subunit protein bL35 | 6 | protein | 65 | Escherichia coli | P0A7Q1 |
| 50S ribosomal protein L36 | 7 | protein | 38 | Escherichia coli | P0A7Q6 |
| 5S rRNA | B | RNA | 120 | Escherichia coli | |
| Large ribosomal subunit protein uL2 | D | protein | 273 | Escherichia coli | P60422 |
| 50S ribosomal protein L3 | E | protein | 209 | Escherichia coli | P60438 |
| 50S ribosomal protein L4 | F | protein | 201 | Escherichia coli | P60723 |
| Large ribosomal subunit protein uL5 | G | protein | 179 | Escherichia coli | P62399 |
44 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>9IOT_1 Large ribosomal subunit protein uL29 (chains 0)
MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEK
AGA
Sequence of entity 2 (1), FASTA
>9IOT_2 Large ribosomal subunit protein uL30 (chains 1)
MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE
Sequence of entity 3 (3), FASTA
>9IOT_3 Large ribosomal subunit protein bL32 (chains 3)
MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK
Sequence of entity 4 (4), FASTA
>9IOT_4 Large ribosomal subunit protein bL33 (chains 4)
MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK
Sequence of entity 5 (5), FASTA
>9IOT_5 50S ribosomal protein L34 (chains 5)
MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK
Sequence of entity 6 (6), FASTA
>9IOT_6 Large ribosomal subunit protein bL35 (chains 6)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA
Sequence of entity 7 (7), FASTA
>9IOT_7 50S ribosomal protein L36 (chains 7)
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG
Sequence of entity 8 (B), FASTA
>9IOT_8 5S rRNA (chains B)
UGCCUGGCGGCAGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU
Sequence of entity 9 (D), FASTA
>9IOT_9 Large ribosomal subunit protein uL2 (chains D)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK
Sequence of entity 10 (E), FASTA
>9IOT_10 50S ribosomal protein L3 (chains E)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 11 (F), FASTA
>9IOT_11 50S ribosomal protein L4 (chains F)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 12 (G), FASTA
>9IOT_12 Large ribosomal subunit protein uL5 (chains G)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 1 |
| MG | Magnesium ion | Mg | 475 |
Primary citation
Molecular basis of RNase I-mediated rRNA degradation regulated by ribosomes. Minami, A., Tanzawa, T., Miyata, T. et al. bioRxiv (2025). DOI 10.1101/2024.07.29.605612
Other PDB entries of the same protein (UniProt P0A7M6 (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)
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