1Y39: 50S ribosomal protein L11

Co-evolution of protein and RNA structures within a highly conserved ribosomal domain. Determined by X-ray diffraction at 2.8 Å resolution. Released 22 Mar 2005.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Geobacillus stearothermophilus
Chains: 4
Atoms: 3,632
Mol. weight: 54.94 kDa
Ligands: 3CO, MG
Released: 22 Mar 2005

Explore 1Y39 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Y39 contains 9 α-helices and 4 β-strands across 2 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	10-18	9
β-strand	33-35	3	1
α-helix	37-47	11
α-helix	56-68	13
β-strand	72-74	3	1

Chain B: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	206-209	4
α-helix	210-217	8
β-strand	233-236	4	2
α-helix	240-247	8
α-helix	248-250	3
α-helix	256-268	13
β-strand	272-275	4	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
58 Nucleotide Ribosomal 23S RNA Domain	C, D	RNA	58
50S ribosomal protein L11	A, B	protein	76	Geobacillus stearothermophilus	P56210 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>1Y39_1 58 Nucleotide Ribosomal 23S RNA Domain (chains C, D)
GCCAGGAUGUAUGCUUAGAAGCAGCAAUCAUUUAAAGAGUGCGUAAUAGCUCACUGGU

Sequence of entity 2 (A, B), FASTA

>1Y39_2 50S ribosomal protein L11 (chains A, B)
FTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAM
RMIEGTARNMGIVVED

Ligands and cofactors

ID	Name	Formula	Copies
3CO	Cobalt (III) ion	Co	2
MG	Magnesium ion	Mg	18

Water and common crystallization additives (GOL, K) are not listed.

Primary citation

Coevolution of Protein and RNA Structures within a Highly Conserved Ribosomal Domain. Dunstan, M.S., Guhathakurta, D., Draper, D.E. et al. Chem Biol (2005) 12:201-206. DOI 10.1016/j.chembiol.2004.11.019 · PubMed

Other PDB entries of the same protein (UniProt P56210 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1HC8 2.8 Å, Crystal structure of a conserved ribosomal protein-RNA complex
1QA6 2.8 Å, Crystal structure of a conserved ribosomal protein-RNA complex
1C04 5.0 Å, Identification of known protein and RNA structures in a 5 a map of the large ribosomal…
1ACI L11 ribosomal protein RNA binding domain, NMR, 20 structures
1FOW NMR structure of L11-C76, the C-terminal domain of 50S ribosomal protein L11, minimized…
1FOX NMR structure of L11-C76, the C-terminal domain of 50S ribosomal protein L11, 33…
1FOY The RNA binding domain of ribosomal protein L11: three-dimensional structure of the…
2FOW The RNA binding domain of ribosomal protein L11: three-dimensional structure of the…

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