› 5wnu

X-ray diffraction
3.4Å resolution

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Released:
DOI: 10.2210/pdb5wnu/pdb
Model geometry
Fit model/data
PDB entry 5wnu coloured by chain, front view.
PDB entry 5wnu coloured by chain, side view.
PDB entry 5wnu coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.
Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD
OpenAccess logo Nat Struct Mol Biol 25 208-216 (2018)
PMID: 29459784

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 23-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-289855 (preferred)
Entry contents:
20 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (23 distinct):
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
Length: 236 amino acids
Theoretical weight: 27.22 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 6-241; Coverage: 92%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Structure domains:
Small ribosomal subunit protein uS3 Chain: C
Molecule details ›
Chain: C
Length: 207 amino acids
Theoretical weight: 22.98 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 2-208; Coverage: 87%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Structure domains:
Small ribosomal subunit protein uS4 Chain: D
Small ribosomal subunit protein uS5 Chain: E
Small ribosomal subunit protein bS6 Chain: F
Small ribosomal subunit protein uS7 Chain: G
Small ribosomal subunit protein uS8 Chain: H
Small ribosomal subunit protein uS9 Chain: I
Small ribosomal subunit protein uS10 Chain: J
Small ribosomal subunit protein uS11 Chain: K
Small ribosomal subunit protein uS12 Chain: L
Small ribosomal subunit protein uS13 Chain: M
Small ribosomal subunit protein uS14 Chain: N
Small ribosomal subunit protein uS15 Chain: O
Small ribosomal subunit protein bS16 Chain: P
Small ribosomal subunit protein uS17 Chain: Q
Small ribosomal subunit protein bS18 Chain: R
Small ribosomal subunit protein uS19 Chain: S
Small ribosomal subunit protein bS20 Chain: T
Small ribosomal subunit protein bTHX Chain: U
16S Ribosomal RNA rRNA Chain: A
RNA (5'-R(*AP*(A2M)P*A)-3') Chain: a
RNA (5'-R(P*UP*(70U)P*UP*UP*(12A)P*A)-3') Chain: b

Ligands and Environments

4 bound ligands:
Ligand MG 252 x MG
Ligand K 22 x K
Ligand B6M 1 x B6M
Ligand ZN 2 x ZN
12 modified residues:
Ligand PSU 3 x PSU
Ligand 7MG 1 x 7MG
Ligand M2G 1 x M2G
Ligand 5MC 4 x 5MC
Ligand 2MG 1 x 2MG
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6
Ligand 0TD 1 x 0TD
Ligand A2M 1 x A2M
Ligand 70U 1 x 70U
Ligand 12A 1 x 12A

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P41212
Unit cell:
a: 400Å b: 400Å c: 173Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.187 0.231

Quick links

Citations

33 review citations

The epitranscriptome beyond m6A.
Wiener et al. (2021)
32 more

1 mention without citation

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.
Choi et al. (2018)