PDBe 2zm6

X-ray diffraction
3.3Å resolution

Crystal structure of the Thermus thermophilus 30S ribosomal subunit

Released:
Source organism: Thermus thermophilus
Entry authors: Kaminishi T, Wang H, Kawazoe M, Ishii R, Schluenzen F, Hanawa-Suetsugu K, Wilson DN, Nomura M, Takemoto C, Shirouzu M, Fucini P, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 21-mer (preferred)
Entry contents:
20 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (21 distinct):
30S ribosomal protein S2 Chain: B
Molecule details ›
Chain: B
Length: 255 amino acids
Theoretical weight: 29.19 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80371 (Residues: 2-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Structure domains:
30S ribosomal protein S3 Chain: C
Molecule details ›
Chain: C
Length: 238 amino acids
Theoretical weight: 26.62 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80372 (Residues: 2-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Structure domains:
30S ribosomal protein S4 Chain: D
Molecule details ›
Chain: D
Length: 208 amino acids
Theoretical weight: 24.24 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80373 (Residues: 2-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
Structure domains:
30S ribosomal protein S5 Chain: E
Molecule details ›
Chain: E
Length: 161 amino acids
Theoretical weight: 17.45 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHQ5 (Residues: 2-162; Coverage: 99%)
Gene names: TTHA1675, rpsE
Sequence domains:
Structure domains:
30S ribosomal protein S6 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
30S ribosomal protein S7 Chain: G
Molecule details ›
Chain: G
Length: 155 amino acids
Theoretical weight: 17.92 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P17291 (Residues: 2-156; Coverage: 99%)
Gene names: TTHA1696, rps7, rpsG
Structure domains: Ribosomal protein S7 domain
30S ribosomal protein S8 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:
30S ribosomal protein S9 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
30S ribosomal protein S10 Chain: J
Molecule details ›
Chain: J
Length: 104 amino acids
Theoretical weight: 11.82 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHN7 (Residues: 2-105; Coverage: 99%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Structure domains: Ribosomal protein S10 domain
30S ribosomal protein S11 Chain: K
Molecule details ›
Chain: K
Length: 128 amino acids
Theoretical weight: 13.61 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80376 (Residues: 2-129; Coverage: 99%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Structure domains: Ribosomal protein S11
30S ribosomal protein S12 Chain: L
Molecule details ›
Chain: L
Length: 131 amino acids
Theoretical weight: 14.51 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-132; Coverage: 99%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Structure domains: Nucleic acid-binding proteins
30S ribosomal protein S13 Chain: M
Molecule details ›
Chain: M
Length: 125 amino acids
Theoretical weight: 14.21 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80377 (Residues: 2-126; Coverage: 99%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Structure domains:
30S ribosomal protein S14 type Z Chain: N
Molecule details ›
Chain: N
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P0DOY6 (Residues: 2-61; Coverage: 98%)
Gene names: TTHA1679, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Structure domains: 30s Ribosomal Protein S14; Chain N
30S ribosomal protein S15 Chain: O
Molecule details ›
Chain: O
Length: 88 amino acids
Theoretical weight: 10.45 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SJ76 (Residues: 2-89; Coverage: 99%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
Structure domains: S15/NS1, RNA-binding
30S ribosomal protein S16 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;
30S ribosomal protein S17 Chain: Q
Molecule details ›
Chain: Q
Length: 104 amino acids
Theoretical weight: 12.19 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: A0A0N0BLS5 (Residues: 2-105; Coverage: 99%)
Gene names: BVI061214_01029, rpsQ
Sequence domains: Ribosomal protein S17
Structure domains: Nucleic acid-binding proteins
30S ribosomal protein S18 Chain: R
Molecule details ›
Chain: R
Length: 87 amino acids
Theoretical weight: 10.11 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SLQ0 (Residues: 2-88; Coverage: 99%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Structure domains: Ribosomal protein S18
30S ribosomal protein S19 Chain: S
Molecule details ›
Chain: S
Length: 92 amino acids
Theoretical weight: 10.47 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHP2 (Residues: 2-93; Coverage: 99%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
Structure domains: 30s Ribosomal Protein S19; Chain A
30S ribosomal protein S20 Chain: T
Molecule details ›
Chain: T
Length: 105 amino acids
Theoretical weight: 11.59 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80380 (Residues: 2-106; Coverage: 99%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Structure domains: Ribosomal protein S20
30S ribosomal protein Thx 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
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1509 nucleotides
Theoretical weight: 489.96 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P41212
Unit cell:
a: 411.5Å b: 411.5Å c: 172.58Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.292 0.292 0.323