4gkj

X-ray diffraction
3.3Å 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 AUG-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 110 10964-9 (2013)
PMID: 23781103

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 23-mer (preferred)
PDBe Complex ID:
PDB-CPX-215960 (preferred)
Entry contents:
20 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (23 distinct):
Small ribosomal subunit protein uS2 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:
Small ribosomal subunit protein uS3 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:
Small ribosomal subunit protein uS4 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:
Small ribosomal subunit protein uS5 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:
Small ribosomal subunit protein bS6 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
Small ribosomal subunit protein uS7 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
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
Structure domains:
Small ribosomal subunit protein uS9 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
Small ribosomal subunit protein uS10 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
Structure domains: Ribosomal protein S10 domain
Small ribosomal subunit protein uS11 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: Ribosomal protein S11
Small ribosomal subunit protein uS12 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
Small ribosomal subunit protein uS13 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 S14 type Z Chain: N
Molecule details ›
Chain: N
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus HB8
Structure domains: 30s Ribosomal Protein S14; Chain N
Small ribosomal subunit protein uS15 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: S15/NS1, RNA-binding
Small ribosomal subunit protein bS16 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
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 HB8
Structure domains: Nucleic acid-binding proteins
Small ribosomal subunit protein bS18 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: Ribosomal protein S18
Small ribosomal subunit protein uS19 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
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: 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: Ribosomal protein S20
Small ribosomal subunit protein bTHX 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
Sequence domains: 30S ribosomal protein Thx
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1513 nucleotides
Theoretical weight: 491.17 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
mRNA A-site fragment Chain: W
Molecule details ›
Chain: W
Length: 6 nucleotides
Theoretical weight: 1.92 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: 400.55Å b: 400.55Å c: 176.19Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.188 0.222