1DFU: E.coli ribosomal protein L25

Crystal structure of e.coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8 a resolution. Determined by X-ray diffraction at 1.8 Å resolution. Released 2 Dec 1999.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Escherichia coli
Chains: 3
Atoms: 1,819
Mol. weight: 23.2 kDa
Ligands: MG
Released: 2 Dec 1999

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

Secondary structure: helices and β-sheets

1DFU contains 5 α-helices and 9 β-strands across 1 chain. 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 P: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	7-8	2	2
α-helix	14-22	9
β-strand	25-31	7	2
α-helix	36-37	2
β-strand	38-43	6	2
α-helix	44-50	7
α-helix	54-57	4
α-helix	60	1
β-strand	61	1	2
β-strand	62-65	4	1
β-strand	68-69	2	1
β-strand	72-79	8	2
β-strand	86-93	8	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5S rRNA	M	RNA	19
5S rRNA	N	RNA	19
Ribosomal protein L25	P	protein	94	Escherichia coli	P68919 (AlphaFold model)

Sequence of entity 1 (M), FASTA

>1DFU_1 5S RRNA (chains M)
CCCAUGCGAGAGUAGGGAC

Sequence of entity 2 (N), FASTA

>1DFU_2 5S RRNA (chains N)
UGCCGAUGGUAGUGUGGGG

Sequence of entity 3 (P), FASTA

>1DFU_3 RIBOSOMAL PROTEIN L25 (chains P)
MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEV
LTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	5

Primary citation

Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution. Lu, M., Steitz, T.A. Proc Natl Acad Sci U S A (2000) 97:2023-2028. DOI 10.1073/pnas.97.5.2023 · PubMed

Other PDB entries of the same protein (UniProt P68919 (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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