› 1hnw

X-ray diffraction
3.4Å resolution

STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH TETRACYCLINE

Released:
DOI: 10.2210/pdb1hnw/pdb
PDB entry 1hnw coloured by chain, front view.
PDB entry 1hnw coloured by chain, side view.
PDB entry 1hnw coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit.
Brodersen DE, Clemons WM, Carter AP, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V
Cell 103 1143-54 (2000)
PMID: 11163189

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 22-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-534327 (preferred)
Entry contents:
20 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (22 distinct):
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Structure domains:
Small ribosomal subunit protein uS3 Chain: C
Molecule details ›
Chain: C
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Structure domains:
Small ribosomal subunit protein uS4 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80373 (Residues: 1-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
Structure domains:
Small ribosomal subunit protein uS5 Chain: E
Molecule details ›
Chain: E
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHQ5 (Residues: 1-162; Coverage: 100%)
Gene names: TTHA1675, rpsE
Sequence domains:
Structure domains:
Small ribosomal subunit protein bS6 Chain: F
Molecule details ›
Chain: F
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
Structure domains: Alpha-Beta Plaits
Small ribosomal subunit protein uS7 Chain: G
Molecule details ›
Chain: G
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P17291 (Residues: 1-156; Coverage: 100%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Structure domains: Ribosomal protein S7 domain
Small ribosomal subunit protein uS8 Chain: H
Molecule details ›
Chain: H
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P0DOY9 (Residues: 1-138; Coverage: 100%)
Gene names: TTHA1678, rpsH
Sequence domains: Ribosomal protein S8
Structure domains:
Small ribosomal subunit protein uS9 Chain: I
Molecule details ›
Chain: I
Length: 128 amino acids
Theoretical weight: 14.43 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80374 (Residues: 1-128; Coverage: 100%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Structure domains: Ribosomal Protein S5; domain 2
Small ribosomal subunit protein uS10 Chain: J
Molecule details ›
Chain: J
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHN7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Structure domains: Ribosomal protein S10 domain
Small ribosomal subunit protein uS11 Chain: K
Molecule details ›
Chain: K
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80376 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Structure domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: L
Molecule details ›
Chain: L
Length: 135 amino acids
Theoretical weight: 14.92 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHN3 (Residues: 1-132; Coverage: 100%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Structure domains: Nucleic acid-binding proteins
Small ribosomal subunit protein uS13 Chain: M
Molecule details ›
Chain: M
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80377 (Residues: 1-126; Coverage: 100%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Structure domains:
Small ribosomal subunit protein uS14 Chain: N
Molecule details ›
Chain: N
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P0DOY6 (Residues: 1-61; Coverage: 100%)
Gene names: TTHA1679, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Structure domains: 30s Ribosomal Protein S14; Chain N
Small ribosomal subunit protein uS15 Chain: O
Molecule details ›
Chain: O
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SJ76 (Residues: 1-89; Coverage: 100%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
Structure domains: S15/NS1, RNA-binding
Small ribosomal subunit protein bS16 Chain: P
Molecule details ›
Chain: P
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
Structure domains: S16 Ribosomal Protein; Chain: A;
Small ribosomal subunit protein uS17 Chain: Q
Molecule details ›
Chain: Q
Length: 105 amino acids
Theoretical weight: 12.32 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P0DOY7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1683, rpsQ
Sequence domains: Ribosomal protein S17
Structure domains: Nucleic acid-binding proteins
Small ribosomal subunit protein bS18 Chain: R
Molecule details ›
Chain: R
Length: 88 amino acids
Theoretical weight: 10.24 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Structure domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: S
Molecule details ›
Chain: S
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHP2 (Residues: 1-93; Coverage: 100%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
Structure domains: 30s Ribosomal Protein S19; Chain A
Small ribosomal subunit protein bS20 Chain: T
Molecule details ›
Chain: T
Length: 106 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Structure domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chain: V
Molecule details ›
Chain: V
Length: 26 amino acids
Theoretical weight: 3.22 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SIH3 (Residues: 2-27; Coverage: 96%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1522 nucleotides
Theoretical weight: 493.96 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
Messenger RNA Chain: X
Molecule details ›
Chain: X
Length: 6 nucleotides
Theoretical weight: 1.79 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 96 x MG
Ligand TAC 2 x TAC
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P41212
Unit cell:
a: 401.158Å b: 401.158Å c: 176.944Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.222 0.264

Quick links

Citations

111 review citations

Ribosome structure and the mechanism of translation.
Ramakrishnan V. (2002)
110 more

14 mentions without citation

Ribosomal protection proteins and their mechanism of tetracycline resistance.
Connell et al. (2003)
13 more