› 4wzd

X-ray diffraction
3.1Å resolution

Complex of 70S ribosome with cognate tRNA-Tyr in the P-site

Released:
DOI: 10.2210/pdb4wzd/pdb
Model geometry
Fit model/data
PDB entry 4wzd coloured by chain, front view.
PDB entry 4wzd coloured by chain, side view.
PDB entry 4wzd coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Structural insights into the translational infidelity mechanism.
Rozov A, Demeshkina N, Westhof E, Yusupov M, Yusupova G
OpenAccess logo Nat Commun 6 7251 (2015)
PMID: 26037619

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
PDBe Complex ID:
PDB-CPX-293959 (preferred)
Entry contents:
49 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (54 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
Small ribosomal subunit protein uS8 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
Small ribosomal subunit protein uS14 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 Chains: 71, 79
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
Large ribosomal subunit protein uL6 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 Chains: I5, M8
Large ribosomal subunit protein bL32 Chains: J5, N8
Large ribosomal subunit protein bL33 Chains: K5, O8
Large ribosomal subunit protein bL34 Chains: L5, P8
Large ribosomal subunit protein bL35 Chains: M5, Q8
16S ribosomal RNA Chains: 13, 1G
tRNA-Tyr Chains: 2K, 2L, 3K, 3L
Messenger RNA Chains: 4K, 4L
23S ribosomal RNA Chains: 14, 1H
5S ribosomal RNA Chains: 16, 1J

Ligands and Environments

2 bound ligands:
Ligand MG 1345 x MG
Ligand ZN 6 x ZN
6 modified residues:
Ligand 4SU 4 x 4SU
Ligand OMG 4 x OMG
Ligand QUO 4 x QUO
Ligand MIA 4 x MIA
Ligand PSU 8 x PSU
Ligand 5MU 4 x 5MU

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 210.7Å b: 448.4Å c: 616.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.227 0.193

Quick links

Citations

19 review citations

The expanding world of tRNA modifications and their disease relevance.
Suzuki T. (2021)
18 more

1 mention without citation

Structural insights into the translational infidelity mechanism.
Rozov et al. (2015)