PDBe 4gkk

X-ray diffraction
3.2Å resolution

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human mitochondrial anticodon stem loop (ASL) of transfer RNA Methionine (TRNAMET) bound to an mRNA with an AUA-codon in the A-site and paromomycin

Released:
Source organism: Thermus thermophilus HB8
Primary publication:
Expanded use of sense codons is regulated by modified cytidines in tRNA.
Proc. Natl. Acad. Sci. U.S.A. (2013)
PMID: 23781103

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 23-mer (preferred)
Entry contents:
20 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (23 distinct):
30S ribosomal protein S2 Chain: B
Molecule details ›
Chain: B
Length: 234 amino acids
Theoretical weight: 26.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 7-240; Coverage: 91%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Structure domains: Helix hairpin bin
30S ribosomal protein S3 Chain: C
Molecule details ›
Chain: C
Length: 206 amino acids
Theoretical weight: 22.86 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 2-207; Coverage: 86%)
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 HB8
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: 150 amino acids
Theoretical weight: 16.33 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 5-154; Coverage: 93%)
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: 155 amino acids
Theoretical weight: 17.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17291 (Residues: 2-156; Coverage: 99%)
Gene names: TTHA1696, rps7, rpsG
Structure domains: Ribosomal Protein S7;
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: Dna Ligase; domain 1
30S ribosomal protein S9 Chain: I
Molecule details ›
Chain: I
Length: 127 amino acids
Theoretical weight: 14.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 2-128; Coverage: 99%)
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: 98 amino acids
Theoretical weight: 11.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 3-100; Coverage: 93%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11 Chain: K
Molecule details ›
Chain: K
Length: 119 amino acids
Theoretical weight: 12.61 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 11-129; Coverage: 92%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Structure domains: Nucleotidyltransferase; domain 5
30S ribosomal protein S12 Chain: L
Molecule details ›
Chain: L
Length: 124 amino acids
Theoretical weight: 13.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-125; Coverage: 94%)
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 HB8
UniProt:
  • Canonical: P80377 (Residues: 2-126; Coverage: 99%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Structure domains:
30S ribosomal protein S15 Chain: O
Molecule details ›
Chain: O
Length: 88 amino acids
Theoretical weight: 10.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 2-89; Coverage: 99%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
Structure domains: Helix Hairpins
30S ribosomal protein S16 Chain: P
Molecule details ›
Chain: P
Length: 83 amino acids
Theoretical weight: 9.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-83; Coverage: 94%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chain: Q
Molecule details ›
Chain: Q
Length: 104 amino acids
Theoretical weight: 12.19 KDa
Source organism: Thermus thermophilus HB8
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: 73 amino acids
Theoretical weight: 8.48 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 16-88; Coverage: 83%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Structure domains: 30s Ribosomal Protein S18
30S ribosomal protein S19 Chain: S
Molecule details ›
Chain: S
Length: 80 amino acids
Theoretical weight: 9.2 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 2-81; Coverage: 86%)
Gene names: TTHA1688, rpsS
Structure domains: 30s Ribosomal Protein S19; Chain A
30S ribosomal protein S20 Chain: T
Molecule details ›
Chain: T
Length: 99 amino acids
Theoretical weight: 10.91 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 8-106; Coverage: 93%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Structure domains: Methane Monooxygenase Hydroxylase; Chain G, domain 1
30S ribosomal protein Thx Chain: V
Molecule details ›
Chain: V
Length: 24 amino acids
Theoretical weight: 2.96 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 2-25; Coverage: 89%)
Gene names: TTHA1396, rpsU
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 HB8
UniProt:
  • Canonical: A0A0N0BLP2 (Residues: 2-61; Coverage: 98%)
Gene names: BVI061214_01033, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Structure domains: 30s Ribosomal Protein S14; Chain N
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1513 nucleotides
Theoretical weight: 491.17 KDa
mRNA A-site fragment Chain: W
Molecule details ›
Chain: W
Length: 6 nucleotides
Theoretical weight: 1.91 KDa
tRNA ASL human mitochondrial Met Chain: X
Molecule details ›
Chain: X
Length: 17 nucleotides
Theoretical weight: 5.41 KDa

Ligands and Environments

3 bound ligands:

2 modified residues:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P41212
Unit cell:
a: 402.37Å b: 402.37Å c: 175.62Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.195 0.236