5D6G: Fragment of ribosomal protein P0

Crystal structure of fragment of ribosomal protein P0 in complex with 74NT 23S RNA from methanococcus jannaschii. Determined by X-ray diffraction at 3.3 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Methanocaldococcus jannaschii
Chains: 2
Atoms: 3,167
Mol. weight: 47.33 kDa
Ligands: MG
Released: 14 Sept 2016

Explore 5D6G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D6G contains 8 α-helices and 11 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 A: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
β-strand	29-34	6	1
α-helix	40-50	11
β-strand	55-58	4	1
α-helix	61-74	14
α-helix	81-85	5
β-strand	92-96	5	1
α-helix	100-109	10
β-strand	112-114	3	2
β-strand	126	1	3
α-helix	140-146	7
β-strand	151-154	4	4
β-strand	157-160	4	4
β-strand	167	1	3
α-helix	181-184	4
β-strand	189-191	3	2
β-strand	194-198	5	1
β-strand	205	1	1
α-helix	208-211	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
50S ribosomal protein L10	A	protein	213	Methanocaldococcus jannaschii	P54049 (AlphaFold model)
23S ribosomal RNA	0	RNA	74	Methanocaldococcus jannaschii

Sequence of entity 1 (A), FASTA

>5D6G_1 50S ribosomal protein L10 (chains A)
MAPWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRAL
KEAAEELNNPKLAELANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCDIKV
EKGSTGMPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKP
IKVGLNILAVYEDGIIYTPDVLKVDEEKLLADI

Sequence of entity 2 (0), FASTA

>5D6G_2 23S ribosomal RNA (chains 0)
GCCUAAGACAGCGGGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAACAGC
UCACCCGUCGAGGC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Primary citation

CRYSTAL STRUCTURE OF FRAGMENT OF RIBOSOMAL PROTEIN P0 IN COMPLEX WITH 74NT 23S RNA FROM METHANOCOCCUS JANNASCHII. Gabdulkhakov, A.G., Mitroshin, I.V., Garber, M.B. To be published.

Other PDB entries of the same protein (UniProt P54049 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3JSY 1.6 Å, N-terminal fragment of ribosomal protein L10 from Methanococcus jannaschii
5D8H 2.8 Å, Crystal structure of the base of the ribosomal P stalk from methanococcus jannaschii…
5DAR 2.9 Å, Crystal structure of the base of the ribosomal P stalk from methanococcus jannaschii

Browse structure collections

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