› 1jgo

X-ray diffraction
5.6Å resolution

The Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGO, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY

Released:
DOI: 10.2210/pdb1jgo/pdb
PDB entry 1jgo coloured by chain, front view.
PDB entry 1jgo coloured by chain, side view.
PDB entry 1jgo coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
The path of messenger RNA through the ribosome.
Yusupova GZ, Yusupov MM, Cate JH, Noller HF
Cell 106 233-41 (2001)
PMID: 11511350

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 25-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-215873 (preferred)
Entry contents:
20 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (24 distinct):
Small ribosomal subunit protein uS2 Chain: E
Molecule details ›
Chain: E
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
Small ribosomal subunit protein uS3 Chain: F
Molecule details ›
Chain: F
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:
Small ribosomal subunit protein uS4 Chain: G
Molecule details ›
Chain: G
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:
Small ribosomal subunit protein uS5 Chain: H
Molecule details ›
Chain: H
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:
Small ribosomal subunit protein bS6 Chain: I
Molecule details ›
Chain: I
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
Small ribosomal subunit protein uS7 Chain: J
Molecule details ›
Chain: J
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
Small ribosomal subunit protein uS8 Chain: K
Molecule details ›
Chain: K
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
Small ribosomal subunit protein uS9 Chain: L
Molecule details ›
Chain: L
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
Small ribosomal subunit protein uS10 Chain: M
Molecule details ›
Chain: M
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
Small ribosomal subunit protein uS11 Chain: N
Molecule details ›
Chain: N
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
Small ribosomal subunit protein uS12 Chain: O
Molecule details ›
Chain: O
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
Small ribosomal subunit protein uS13 Chain: P
Molecule details ›
Chain: P
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
Small ribosomal subunit protein uS14 Chain: Q
Molecule details ›
Chain: Q
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
Small ribosomal subunit protein uS15 Chain: R
Molecule details ›
Chain: R
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
Small ribosomal subunit protein bS16 Chain: S
Molecule details ›
Chain: S
Length: 91 amino acids
Theoretical weight: 10.81 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-17, 18-88; Coverage: 100%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: T
Molecule details ›
Chain: T
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
Small ribosomal subunit protein bS18 Chain: U
Molecule details ›
Chain: U
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
Small ribosomal subunit protein uS19 Chain: V
Molecule details ›
Chain: V
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
Small ribosomal subunit protein bS20 Chain: W
Molecule details ›
Chain: W
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
Small ribosomal subunit protein bTHX Chain: X
Molecule details ›
Chain: X
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
tRNA(Phe) Chains: B, C
Molecule details ›
Chains: B, C
Length: 76 nucleotides
Theoretical weight: 24.89 KDa
Sequence domains: tRNA
tRNA(Phe) Chain: D
Molecule details ›
Chain: D
Length: 74 nucleotides
Theoretical weight: 23.73 KDa
Sequence domains: tRNA
MESSENGER RNA MK27 Chain: 1
Molecule details ›
Chain: 1
Length: 27 nucleotides
Theoretical weight: 8.75 KDa

Ligands and Environments

No bound ligands
12 modified residues:
Ligand 2MG 2 x 2MG
Ligand H2U 6 x H2U
Ligand M2G 2 x M2G
Ligand OMC 2 x OMC
Ligand OMG 2 x OMG
Ligand YG 2 x YG
Ligand PSU 5 x PSU
Ligand 5MC 5 x 5MC
Ligand 7MG 2 x 7MG
Ligand 5MU 3 x 5MU
Ligand 1MA 2 x 1MA
Ligand 4SU 1 x 4SU

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: I422
Unit cell:
a: 507.2Å b: 507.2Å c: 803.66Å
α: 90° β: 90° γ: 90°

Quick links

Citations

76 review citations

Regulation of translation via mRNA structure in prokaryotes and eukaryotes.
Kozak M. (2005)
75 more

9 mentions without citation

The mechanism of eukaryotic translation initiation and principles of its regulation.
Jackson et al. (2010)
8 more