› 5el5

X-ray diffraction
3.15Å resolution

Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position

Released:
DOI: 10.2210/pdb5el5/pdb
Model geometry
Fit model/data
PDB entry 5el5 coloured by chain, front view.
PDB entry 5el5 coloured by chain, side view.
PDB entry 5el5 coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.
Rozov A, Demeshkina N, Khusainov I, Westhof E, Yusupov M, Yusupova G
OpenAccess logo Nat Commun 7 10457 (2016)
PMID: 26791911

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero 55-mer (preferred)
hetero 53-mer
PDBe Complex ID:
PDB-CPX-148012 (preferred)
Entry contents:
48 distinct polypeptide molecules
9 distinct RNA molecules
Macromolecules (57 distinct):
Small ribosomal subunit protein uS2 Chains: 12, 1E
Molecule details ›
Chains: 12, 1E
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: 22, 2E
Molecule details ›
Chains: 22, 2E
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: 32, 3E
Small ribosomal subunit protein uS5 Chains: 42, 4E
Small ribosomal subunit protein bS6 Chains: 52, 5E
Small ribosomal subunit protein uS7 Chains: 62, 6E
30S ribosomal protein S8 Chains: 72, 7E
Small ribosomal subunit protein uS9 Chains: 82, 8E
Small ribosomal subunit protein uS10 Chains: 1A, 1I
Small ribosomal subunit protein uS11 Chains: 2A, 2I
Small ribosomal subunit protein uS12 Chains: 3A, 3I
Small ribosomal subunit protein uS13 Chains: 4A, 4I
30S ribosomal protein S14 type Z Chains: 5A, 5I
Small ribosomal subunit protein uS15 Chains: 6A, 6I
Small ribosomal subunit protein bS16 Chains: 7A, 7I
30S ribosomal protein S17 Chains: 8A, 8I
Small ribosomal subunit protein bS18 Chains: 9A, 9I
Small ribosomal subunit protein uS19 Chains: AA, AI
Small ribosomal subunit protein bS20 Chains: BA, BI
Small ribosomal subunit protein bTHX Chains: 1B, 1F
Large ribosomal subunit protein uL1 Chain: 71
Large ribosomal subunit protein uL2 Chains: 11, 19
Large ribosomal subunit protein uL3 Chains: 21, 29
Large ribosomal subunit protein uL4 Chains: 31, 39
Large ribosomal subunit protein uL5 Chains: 41, 49
50S ribosomal protein L6 Chains: 51, 59
Large ribosomal subunit protein bL9 Chains: 61, 69
Large ribosomal subunit protein uL13 Chains: 15, 58
Large ribosomal subunit protein uL14 Chains: 25, 68
Large ribosomal subunit protein uL15 Chains: 35, 78
Large ribosomal subunit protein uL16 Chains: 45, 88
Large ribosomal subunit protein bL17 Chains: 55, 98
Large ribosomal subunit protein uL18 Chains: 65, A8
Large ribosomal subunit protein bL19 Chains: 75, B8
Large ribosomal subunit protein bL20 Chains: 85, C8
Large ribosomal subunit protein bL21 Chains: 95, D8
Large ribosomal subunit protein uL22 Chains: A5, E8
Large ribosomal subunit protein uL23 Chains: B5, F8
Large ribosomal subunit protein uL24 Chains: C5, G8
Large ribosomal subunit protein bL25 Chains: D5, H8
Large ribosomal subunit protein bL27 Chains: E5, I8
Large ribosomal subunit protein bL28 Chains: F5, J8
Large ribosomal subunit protein uL29 Chains: G5, K8
Large ribosomal subunit protein uL30 Chains: H5, L8
Large ribosomal subunit protein bL31 Chain: M8
Large ribosomal subunit protein bL32 Chains: J5, N8
Large ribosomal subunit protein bL34 Chains: L5, P8
Large ribosomal subunit protein bL35 Chains: M5, Q8
16S ribosomal RNA Chains: 13, 1G
tRNALys Chain: 1K
tRNAfMet Chains: 2K, 2L
tRNALys Chain: 3K
Messenger RNA Chains: 4K, 4L
23S ribosomal RNA Chains: 14, 1H
5S ribosomal RNA Chains: 16, 1J
tRNALys Chain: 1L
tRNALys Chain: 3L

Ligands and Environments

3 bound ligands:
Ligand MG 1182 x MG
Ligand SF4 2 x SF4
Ligand ZN 4 x ZN
8 modified residues:
Ligand U8U 1 x U8U
Ligand T6A 1 x T6A
Ligand PSU 7 x PSU
Ligand 7MG 2 x 7MG
Ligand 5MU 4 x 5MU
Ligand 4SU 2 x 4SU
Ligand OMC 2 x OMC
Ligand G7M 2 x G7M

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 208.4Å b: 447.1Å c: 616.9Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.198 0.254

Quick links

Citations

22 review citations

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.
Atkins et al. (2016)
21 more

1 mention without citation

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.
Rozov et al. (2016)