› 8ip9

Electron Microscopy
3Å resolution

Wheat 40S ribosome in complex with a tRNAi

Released:
DOI: 10.2210/pdb8ip9/pdb
PDB entry 8ip9 coloured by chain, front view.
PDB entry 8ip9 coloured by chain, side view.
PDB entry 8ip9 coloured by chain, top view.
Source organisms:
Primary publication:
Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Tanaka M, Yokoyama T, Saito H, Nishimoto M, Tsuda K, Sotta N, Shigematsu H, Shirouzu M, Iwasaki S, Ito T, Fujiwara T
Nat Chem Biol (2024)
PMID: 38267667
Related structures: EMD-35635

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 35-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-278901 (preferred)
Entry contents:
32 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (35 distinct):
40S ribosomal protein S24 Chain: ba
Molecule details ›
Chain: ba
Length: 137 amino acids
Theoretical weight: 15.74 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6PK86 (Residues: 1-137; Coverage: 100%)
Sequence domains: Ribosomal protein S24e
40S ribosomal protein S8 Chain: ca
Molecule details ›
Chain: ca
Length: 225 amino acids
Theoretical weight: 25.34 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6AYT7 (Residues: 1-225; Coverage: 100%)
Sequence domains: Ribosomal protein S8e
Plectin/eS10 N-terminal domain-containing protein Chain: da
Molecule details ›
Chain: da
Length: 188 amino acids
Theoretical weight: 20.46 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5AUH7 (Residues: 1-188; Coverage: 100%)
Sequence domains: Plectin/S10 domain
40S ribosomal protein S23 Chain: ga
Molecule details ›
Chain: ga
Length: 142 amino acids
Theoretical weight: 15.7 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5FV77 (Residues: 1-142; Coverage: 100%)
Gene names: LOC123059459, LOC123105643, LOC123123461
Sequence domains: Ribosomal protein S12/S23
RACK1 Chain: ha
Molecule details ›
Chain: ha
Length: 332 amino acids
Theoretical weight: 36.2 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5D4F5 (Residues: 1-332; Coverage: 100%)
Sequence domains: WD domain, G-beta repeat
30S ribosomal protein S3, chloroplastic Chain: ia
Molecule details ›
Chain: ia
Length: 227 amino acids
Theoretical weight: 25.41 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q8L804 (Residues: 1-227; Coverage: 100%)
Sequence domains:
40S ribosomal protein S4 Chain: ja
Molecule details ›
Chain: ja
Length: 265 amino acids
Theoretical weight: 30.01 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A1D5SLI4 (Residues: 1-265; Coverage: 100%)
Gene name: LOC123191404
Sequence domains:
Small ribosomal subunit protein uS7c Chain: ka
Molecule details ›
Chain: ka
Length: 200 amino acids
Theoretical weight: 22.35 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5D067 (Residues: 1-200; Coverage: 100%)
Sequence domains: Ribosomal protein S7p/S5e
40S ribosomal protein S16 Chain: la
Molecule details ›
Chain: la
Length: 149 amino acids
Theoretical weight: 16.87 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6HX49 (Residues: 1-149; Coverage: 100%)
Gene name: LOC123086419
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 domain-containing protein Chain: ma
Molecule details ›
Chain: ma
Length: 127 amino acids
Theoretical weight: 14.13 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: U5HTD8 (Residues: 1-127; Coverage: 100%)
Gene name: LOC123170464
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11, chloroplastic Chain: na
Molecule details ›
Chain: na
Length: 151 amino acids
Theoretical weight: 16.4 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6SS17 (Residues: 1-151; Coverage: 100%)
Gene name: LOC123157862
Sequence domains: Ribosomal protein S11
Putative ribosomal protein S18 Chain: oa
Molecule details ›
Chain: oa
Length: 152 amino acids
Theoretical weight: 17.7 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q8L806 (Residues: 1-152; Coverage: 100%)
Gene name: LOC123105378
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS15 N-terminal domain-containing protein Chain: pa
Molecule details ›
Chain: pa
Length: 151 amino acids
Theoretical weight: 17.1 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5XUU9 (Residues: 1-151; Coverage: 100%)
Sequence domains:
40S ribosomal protein S17 Chain: qa
Molecule details ›
Chain: qa
Length: 143 amino acids
Theoretical weight: 16.52 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B5YWZ3 (Residues: 1-143; Coverage: 100%)
Sequence domains: Ribosomal S17
40S ribosomal protein S19 Chain: ra
Molecule details ›
Chain: ra
Length: 155 amino acids
Theoretical weight: 17.1 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5FWF5 (Residues: 1-155; Coverage: 100%)
Sequence domains: Ribosomal protein S19e
40S ribosomal protein uS19 Chain: sa
Molecule details ›
Chain: sa
Length: 154 amino acids
Theoretical weight: 17.42 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5ASA4 (Residues: 1-154; Coverage: 100%)
Sequence domains: Ribosomal protein S19
40S ribosomal protein S25 Chain: ta
Molecule details ›
Chain: ta
Length: 108 amino acids
Theoretical weight: 12.09 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5EP45 (Residues: 1-108; Coverage: 100%)
Gene name: LOC123090517
Sequence domains: S25 ribosomal protein
S28 ribosomal protein Chain: ua
Molecule details ›
Chain: ua
Length: 86 amino acids
Theoretical weight: 9.82 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q7X9K4 (Residues: 1-86; Coverage: 100%)
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein uS8c Chain: va
Molecule details ›
Chain: va
Length: 129 amino acids
Theoretical weight: 14.92 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A077RZD1 (Residues: 1-129; Coverage: 100%)
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS14 Chain: wa
Molecule details ›
Chain: wa
Length: 56 amino acids
Theoretical weight: 6.39 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K3 (Residues: 1-56; Coverage: 100%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
40S ribosomal protein S27 Chain: xa
Molecule details ›
Chain: xa
Length: 86 amino acids
Theoretical weight: 9.58 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5HZ68 (Residues: 1-86; Coverage: 100%)
Gene names: LOC123091157, LOC123165679
Sequence domains: Ribosomal protein S27
40S ribosomal protein S30 Chain: ya
Molecule details ›
Chain: ya
Length: 62 amino acids
Theoretical weight: 6.93 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6S9M7 (Residues: 1-62; Coverage: 100%)
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein uS2 Chain: za
Molecule details ›
Chain: za
Length: 308 amino acids
Theoretical weight: 33.3 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5E2W7 (Residues: 1-308; Coverage: 100%)
Gene names: LOC123093407, LOC123098682
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS1 Chain: bb
Molecule details ›
Chain: bb
Length: 263 amino acids
Theoretical weight: 30.04 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6IU74 (Residues: 1-263; Coverage: 100%)
Sequence domains: Ribosomal S3Ae family
40S ribosomal protein S21 Chain: cb
Molecule details ›
Chain: cb
Length: 82 amino acids
Theoretical weight: 9.19 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5EL62 (Residues: 1-82; Coverage: 100%)
Sequence domains: Ribosomal protein S21e
40S ribosomal protein S26 Chain: db
Molecule details ›
Chain: db
Length: 156 amino acids
Theoretical weight: 16.58 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6LWE1 (Residues: 1-156; Coverage: 100%)
Sequence domains: Ribosomal protein S26e
30S ribosomal protein S4, chloroplastic Chain: eb
Molecule details ›
Chain: eb
Length: 195 amino acids
Theoretical weight: 22.53 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5FPA7 (Residues: 1-195; Coverage: 100%)
Gene name: LOC543424
Sequence domains:
S5 DRBM domain-containing protein Chain: fb
Molecule details ›
Chain: fb
Length: 274 amino acids
Theoretical weight: 30 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6LVN2 (Residues: 1-274; Coverage: 100%)
Sequence domains:
40S ribosomal protein S6 Chain: gb
Molecule details ›
Chain: gb
Length: 250 amino acids
Theoretical weight: 28.49 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A2X0SLI3 (Residues: 1-250; Coverage: 100%)
Sequence domains: Ribosomal protein S6e
40S ribosomal protein S7 Chain: hb
Molecule details ›
Chain: hb
Length: 192 amino acids
Theoretical weight: 22.3 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K2 (Residues: 1-192; Coverage: 100%)
Gene name: LOC123085612
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chain: ib
Molecule details ›
Chain: ib
Length: 159 amino acids
Theoretical weight: 17.84 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5BFB7 (Residues: 1-159; Coverage: 100%)
Sequence domains:
Small ribosomal subunit protein eS32 Chain: IB
Molecule details ›
Chain: IB
Length: 25 amino acids
Theoretical weight: 3.45 KDa
Source organism: Oryza sativa
UniProt:
  • Canonical: P62125 (Residues: 1-25; Coverage: 100%)
Gene names: LOC_Os03g56878, OSJNBa0091J19.8, Os03g0781500, Os03g0781501, RPL41
Sequence domains: Ribosomal protein L41
18S Ribosomal RNA Chain: aa
Molecule details ›
Chain: aa
Length: 1810 nucleotides
Theoretical weight: 583.61 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
Messenger RNA Chain: al
Molecule details ›
Chain: al
Length: 7 nucleotides
Theoretical weight: 2.23 KDa
tRNAi Chain: cl
Molecule details ›
Chain: cl
Length: 75 nucleotides
Theoretical weight: 24.45 KDa
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand MG 84 x MG
Ligand ZN 2 x ZN
8 modified residues:
Ligand 1MG 1 x 1MG
Ligand 2MG 2 x 2MG
Ligand PSU 2 x PSU
Ligand MIA 1 x MIA
Ligand G7M 1 x G7M
Ligand H2U 1 x H2U
Ligand 5MC 2 x 5MC
Ligand 1MA 1 x 1MA

Experiments and Validation Details

Entry percentile scores
Resolution: 3Å
Relevant EMDB volumes: EMD-35635

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