5DAR: 50S ribosomal protein L10

Name: PDB 5DAR: Crystal structure of the base of the ribosomal P stalk from methanococcus jannaschii
Published: 2016-09-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosomal protein

Crystal structure of the base of the ribosomal P stalk from methanococcus jannaschii. Determined by X-ray diffraction at 2.9 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Methanocaldococcus jannaschii
Chains: 6
Atoms: 8,414
Mol. weight: 130.09 kDa
Ligands: MG
Released: 14 Sept 2016

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

Secondary structure: helices and β-sheets

5DAR contains 33 α-helices and 35 β-strands across 4 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 B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
β-strand	29-34	6	1
α-helix	40-49	10
β-strand	55-58	4	1
α-helix	61-75	15
α-helix	78-81	4
α-helix	84-86	3
β-strand	91-96	6	1
α-helix	100-109	10
β-strand	111-114	4	2
α-helix	115-117	3
β-strand	121	1	3
β-strand	172	1	3
α-helix	175-184	10
β-strand	189-192	4	2
β-strand	194-199	6	1
β-strand	204-205	2	1
α-helix	207-210	4

Chain C: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	4
α-helix	21-24	4
α-helix	31-41	11
β-strand	49-57	9	4
β-strand	62-67	6	4
α-helix	72-80	9
β-strand	95-97	3	5
α-helix	99-109	11
α-helix	118-129	12
β-strand	134-136	3	5
β-strand	139	1	5
α-helix	141-149	9

Chain E: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
β-strand	29-34	6	6
α-helix	40-49	10
β-strand	54-58	5	6
α-helix	61-70	10
α-helix	84-86	3
β-strand	91-96	6	6
α-helix	100-109	10
β-strand	111-114	4	7
β-strand	120-121	2	8
β-strand	126	1	9
β-strand	131-132	2	10
α-helix	135-136	2
α-helix	140-146	7
β-strand	151-154	4	10
β-strand	157-160	4	10
β-strand	167	1	9
β-strand	172-173	2	8
α-helix	174	1
α-helix	175-184	10
β-strand	189-192	4	7
β-strand	194-199	6	6
β-strand	204	1	6

Chain F: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	11
α-helix	20-24	5
α-helix	25-27	3
α-helix	31-41	11
β-strand	49-57	9	11
β-strand	63-67	5	11
α-helix	68-71	4
α-helix	72-80	9
β-strand	96-97	2	12
α-helix	99-108	10
α-helix	118-129	12
β-strand	135-136	2	12
β-strand	139	1	12
α-helix	141-149	9
α-helix	154-157	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
74 nt fragment of 23S rRNA	A, D	RNA	74	Methanocaldococcus jannaschii
50S ribosomal protein L10	B, E	protein	213	Methanocaldococcus jannaschii	P54049 (AlphaFold model)
50S ribosomal protein L11	C, F	protein	161	Methanocaldococcus jannaschii	P54030 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5DAR_1 74 nt fragment of 23S rRNA (chains A, D)
GCCUAAGACAGCGGGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAACAGC
UCACCCGUCGAGGC

Sequence of entity 2 (B, E), FASTA

>5DAR_2 50S ribosomal protein L10 (chains B, E)
MAPWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRAL
KEAAEELNNPKLAELANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCDIKV
EKGSTGMPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKP
IKVGLNILAVYEDGIIYTPDVLKVDEEKLLADI

Sequence of entity 3 (C, F), FASTA

>5DAR_3 50S ribosomal protein L11 (chains C, F)
MAKEVVEVLVTGGRATAGPPLGPAIGPLGVNVMQVVKEINEKTKDYEGMQVPVKVIVDTE
TRKFEIEVGIPPTTALIKKELGIETAAHEPRHEVVGNLTLEQVIKIAKMKKDAMLSYTLK
NAVKEVLGTCGSMGVTVEGKDPKEVQKEIDAGVYDEYFKEE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	8

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

Primary citation

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK 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…
5D6G 3.3 Å, Crystal structure of fragment of ribosomal protein P0 in complex with 74NT 23S RNA from…

Browse structure collections

About this viewer

MolViewer shows 5DAR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.