› 5lmp

Electron Microscopy
5.35Å resolution

Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1C)

Released:
DOI: 10.2210/pdb5lmp/pdb
PDB entry 5lmp coloured by chain, front view.
PDB entry 5lmp coloured by chain, side view.
PDB entry 5lmp coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation.
Hussain T, Llácer JL, Wimberly BT, Kieft JS, Ramakrishnan V
OpenAccess logo Cell 167 133-144.e13 (2016)
PMID: 27662086
Related structures: EMD-4075

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 24-mer (preferred)
PDBe Complex ID:
PDB-CPX-250078 (preferred)
Entry contents:
22 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (24 distinct):
Small ribosomal subunit protein uS2 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
Small ribosomal subunit protein uS3 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:
Small ribosomal subunit protein uS4 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:
Small ribosomal subunit protein uS5 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:
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
Small ribosomal subunit protein uS7 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
Small ribosomal subunit protein uS8 Chain: H
Molecule details ›
Chain: H
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY9 (Residues: 1-138; Coverage: 100%)
Gene names: TTHA1678, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 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
Small ribosomal subunit protein uS10 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
Small ribosomal subunit protein uS11 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
Small ribosomal subunit protein uS12 Chain: L
Molecule details ›
Chain: L
Length: 132 amino acids
Theoretical weight: 14.64 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 1-132; Coverage: 100%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 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
Small ribosomal subunit protein uS14 Chain: N
Molecule details ›
Chain: N
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB8
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: 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
Small ribosomal subunit protein bS16 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
Small ribosomal subunit protein uS17 Chain: Q
Molecule details ›
Chain: Q
Length: 105 amino acids
Theoretical weight: 12.33 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1683, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 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
Small ribosomal subunit protein uS19 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
Small ribosomal subunit protein bS20 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
Small ribosomal subunit protein bTHX Chain: V
Molecule details ›
Chain: V
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
Translation initiation factor IF-1 Chain: W
Molecule details ›
Chain: W
Length: 72 amino acids
Theoretical weight: 8.25 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SHR1 (Residues: 1-72; Coverage: 100%)
Gene names: TTHA1669, infA
Sequence domains: Translation initiation factor 1A / IF-1
Translation initiation factor IF-3 Chain: X
Molecule details ›
Chain: X
Length: 171 amino acids
Theoretical weight: 19.9 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SKU2 (Residues: 1-171; Coverage: 100%)
Gene names: TTHA0551, infC
Sequence domains:
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1522 nucleotides
Theoretical weight: 493.96 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
Messenger RNA Chain: Y
Molecule details ›
Chain: Y
Length: 39 nucleotides
Theoretical weight: 12.53 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 108 x MG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.35Å
Relevant EMDB volumes: EMD-4075
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

17 review citations

Structural Insights into the Mechanism of Scanning and Start Codon Recognition in Eukaryotic Translation Initiation.
Hinnebusch AG. (2017)
16 more

6 mentions without citation

Measurement of atom resolvability in cryo-EM maps with Q-scores.
Pintilie et al. (2020)
5 more