PDBe 4duy

X-ray diffraction
3.39Å resolution

Crystal structure of the Thermus thermophilus 30S ribosomal subunit with a 16S rRNA mutation, U13C

Released:
Source organism: Thermus thermophilus HB8
Entry authors: Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G

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: 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
Structure domains:
30S ribosomal protein S3 Chain: C
Molecule details ›
Chain: C
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:
Structure domains:
30S ribosomal protein S4 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80373 (Residues: 1-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
Structure domains:
30S ribosomal protein S5 Chain: E
Molecule details ›
Chain: E
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 1-162; Coverage: 100%)
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 HB8
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: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB8
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
30S ribosomal protein S8 Chain: H
Molecule details ›
Chain: H
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0M9AFS9 (Residues: 1-138; Coverage: 100%)
Gene names: BVI061214_01034, rpsH
Sequence domains: Ribosomal protein S8
Structure domains:
30S ribosomal protein S9 Chain: I
Molecule details ›
Chain: I
Length: 128 amino acids
Theoretical weight: 14.41 KDa
Source organism: Thermus thermophilus HB8
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: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 1-105; Coverage: 100%)
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: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 1-129; Coverage: 100%)
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: 135 amino acids
Theoretical weight: 14.97 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 1-132; Coverage: 100%)
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: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 1-126; Coverage: 100%)
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: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0N0BLP2 (Residues: 1-61; Coverage: 100%)
Gene names: BVI061214_01033, 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: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 1-89; Coverage: 100%)
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 HB8
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: 105 amino acids
Theoretical weight: 12.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0N0BLS5 (Residues: 1-105; Coverage: 100%)
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: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
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: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB8
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
30S ribosomal protein S20 Chain: T
Molecule details ›
Chain: T
Length: 106 amino acids
Theoretical weight: 11.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Structure domains: Ribosomal protein S20
30S ribosomal protein Thx Chain: U
Molecule details ›
Chain: U
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 1-27; Coverage: 100%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1522 nucleotides
Theoretical weight: 494.17 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P41212
Unit cell:
a: 402.518Å b: 402.518Å c: 175.892Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.159 0.202