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Wheat 40S ribosome in complex with a tRNAi

Electron Microscopy
3Å resolution
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:
Assembly composition:
hetero 35-mer (preferred)
Entry contents: 32 distinct polypeptide molecules
3 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: 30S ribosome subunit,40S ribosome subunit and RACK1 and RNA
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Multimeric state: hetero 35-mer
Accessible surface area: 385161.54 Å2
Buried surface area: 183234.62 Å2
Dissociation area: 1,949.45 Å2
Dissociation energy (ΔGdiss): 4.1 kcal/mol
Dissociation entropy (TΔSdiss): 11.66 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-278901

Macromolecules

40S ribosomal protein S24
Chain: ba
Length: 137 amino acids
Theoretical weight: 15.74 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6PK86 (Residues: 1-137; Coverage: 100%)
Pfam: Ribosomal protein S24e
40S ribosomal protein S24 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S24 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S24 in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S8
Chain: ca
Length: 225 amino acids
Theoretical weight: 25.34 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6AYT7 (Residues: 1-225; Coverage: 100%)
Pfam: Ribosomal protein S8e
40S ribosomal protein S8 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S8 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S8 in PDB entry 8ip9, assembly 1, top view.
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Plectin/eS10 N-terminal domain-containing protein
Chain: da
Length: 188 amino acids
Theoretical weight: 20.46 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5AUH7 (Residues: 1-188; Coverage: 100%)
Pfam: Plectin/S10 domain
Plectin/eS10 N-terminal domain-containing protein in PDB entry 8ip9, assembly 1, front view.
Plectin/eS10 N-terminal domain-containing protein in PDB entry 8ip9, assembly 1, side view.
Plectin/eS10 N-terminal domain-containing protein in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S23
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
Pfam: Ribosomal protein S12/S23
40S ribosomal protein S23 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S23 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S23 in PDB entry 8ip9, assembly 1, top view.
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RACK1
Chain: ha
Length: 332 amino acids
Theoretical weight: 36.2 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5D4F5 (Residues: 1-332; Coverage: 100%)
Pfam: WD domain, G-beta repeat
RACK1 in PDB entry 8ip9, assembly 1, front view.
RACK1 in PDB entry 8ip9, assembly 1, side view.
RACK1 in PDB entry 8ip9, assembly 1, top view.
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30S ribosomal protein S3, chloroplastic
Chain: ia
Length: 227 amino acids
Theoretical weight: 25.41 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q8L804 (Residues: 1-227; Coverage: 100%)
Pfam:
30S ribosomal protein S3, chloroplastic in PDB entry 8ip9, assembly 1, front view.
30S ribosomal protein S3, chloroplastic in PDB entry 8ip9, assembly 1, side view.
30S ribosomal protein S3, chloroplastic in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S4
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
Pfam:
40S ribosomal protein S4 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S4 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S4 in PDB entry 8ip9, assembly 1, top view.
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Small ribosomal subunit protein uS7c
Chain: ka
Length: 200 amino acids
Theoretical weight: 22.35 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5D067 (Residues: 1-200; Coverage: 100%)
Pfam: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS7c in PDB entry 8ip9, assembly 1, front view.
Small ribosomal subunit protein uS7c in PDB entry 8ip9, assembly 1, side view.
Small ribosomal subunit protein uS7c in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S16
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
Pfam: Ribosomal protein S9/S16
40S ribosomal protein S16 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S16 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S16 in PDB entry 8ip9, assembly 1, top view.
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Small ribosomal subunit protein uS10 domain-containing protein
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
Pfam: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS10 domain-containing protein in PDB entry 8ip9, assembly 1, front view.
Small ribosomal subunit protein uS10 domain-containing protein in PDB entry 8ip9, assembly 1, side view.
Small ribosomal subunit protein uS10 domain-containing protein in PDB entry 8ip9, assembly 1, top view.
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30S ribosomal protein S11, chloroplastic
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
Pfam: Ribosomal protein S11
30S ribosomal protein S11, chloroplastic in PDB entry 8ip9, assembly 1, front view.
30S ribosomal protein S11, chloroplastic in PDB entry 8ip9, assembly 1, side view.
30S ribosomal protein S11, chloroplastic in PDB entry 8ip9, assembly 1, top view.
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Putative ribosomal protein S18
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
Pfam: Ribosomal protein S13/S18
Putative ribosomal protein S18 in PDB entry 8ip9, assembly 1, front view.
Putative ribosomal protein S18 in PDB entry 8ip9, assembly 1, side view.
Putative ribosomal protein S18 in PDB entry 8ip9, assembly 1, top view.
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Small ribosomal subunit protein uS15 N-terminal domain-containing protein
Chain: pa
Length: 151 amino acids
Theoretical weight: 17.1 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5XUU9 (Residues: 1-151; Coverage: 100%)
Pfam:
Small ribosomal subunit protein uS15 N-terminal domain-containing protein in PDB entry 8ip9, assembly 1, front view.
Small ribosomal subunit protein uS15 N-terminal domain-containing protein in PDB entry 8ip9, assembly 1, side view.
Small ribosomal subunit protein uS15 N-terminal domain-containing protein in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S17
Chain: qa
Length: 143 amino acids
Theoretical weight: 16.52 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B5YWZ3 (Residues: 1-143; Coverage: 100%)
Pfam: Ribosomal S17
40S ribosomal protein S17 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S17 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S17 in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S19
Chain: ra
Length: 155 amino acids
Theoretical weight: 17.1 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5FWF5 (Residues: 1-155; Coverage: 100%)
Pfam: Ribosomal protein S19e
40S ribosomal protein S19 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S19 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S19 in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein uS19
Chain: sa
Length: 154 amino acids
Theoretical weight: 17.42 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5ASA4 (Residues: 1-154; Coverage: 100%)
Pfam: Ribosomal protein S19
40S ribosomal protein uS19 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein uS19 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein uS19 in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S25
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
Pfam: S25 ribosomal protein
40S ribosomal protein S25 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S25 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S25 in PDB entry 8ip9, assembly 1, top view.
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S28 ribosomal protein
Chain: ua
Length: 86 amino acids
Theoretical weight: 9.82 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q7X9K4 (Residues: 1-86; Coverage: 100%)
Pfam: Ribosomal protein S28e
S28 ribosomal protein in PDB entry 8ip9, assembly 1, front view.
S28 ribosomal protein in PDB entry 8ip9, assembly 1, side view.
S28 ribosomal protein in PDB entry 8ip9, assembly 1, top view.
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Small ribosomal subunit protein uS8c
Chain: va
Length: 129 amino acids
Theoretical weight: 14.92 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A077RZD1 (Residues: 1-129; Coverage: 100%)
Pfam: Ribosomal protein S8
Small ribosomal subunit protein uS8c in PDB entry 8ip9, assembly 1, front view.
Small ribosomal subunit protein uS8c in PDB entry 8ip9, assembly 1, side view.
Small ribosomal subunit protein uS8c in PDB entry 8ip9, assembly 1, top view.
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Small ribosomal subunit protein uS14
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
Pfam: Ribosomal protein S14p/S29e
40S ribosomal protein S29 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S29 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S29 in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S27
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
Pfam: Ribosomal protein S27
40S ribosomal protein S27 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S27 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S27 in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S30
Chain: ya
Length: 62 amino acids
Theoretical weight: 6.93 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6S9M7 (Residues: 1-62; Coverage: 100%)
Pfam: Ribosomal protein S30
40S ribosomal protein S30 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S30 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S30 in PDB entry 8ip9, assembly 1, top view.
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Small ribosomal subunit protein uS2
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
Pfam: Ribosomal protein S2
Small ribosomal subunit protein uS2 in PDB entry 8ip9, assembly 1, front view.
Small ribosomal subunit protein uS2 in PDB entry 8ip9, assembly 1, side view.
Small ribosomal subunit protein uS2 in PDB entry 8ip9, assembly 1, top view.
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Small ribosomal subunit protein eS1
Chain: bb
Length: 263 amino acids
Theoretical weight: 30.04 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6IU74 (Residues: 1-263; Coverage: 100%)
Pfam: Ribosomal S3Ae family
Small ribosomal subunit protein eS1 in PDB entry 8ip9, assembly 1, front view.
Small ribosomal subunit protein eS1 in PDB entry 8ip9, assembly 1, side view.
Small ribosomal subunit protein eS1 in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S21
Chain: cb
Length: 82 amino acids
Theoretical weight: 9.19 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5EL62 (Residues: 1-82; Coverage: 100%)
Pfam: Ribosomal protein S21e
40S ribosomal protein S21 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S21 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S21 in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S26
Chain: db
Length: 156 amino acids
Theoretical weight: 16.58 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6LWE1 (Residues: 1-156; Coverage: 100%)
Pfam: Ribosomal protein S26e
40S ribosomal protein S26 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S26 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S26 in PDB entry 8ip9, assembly 1, top view.
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30S ribosomal protein S4, chloroplastic
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
Pfam:
30S ribosomal protein S4, chloroplastic in PDB entry 8ip9, assembly 1, front view.
30S ribosomal protein S4, chloroplastic in PDB entry 8ip9, assembly 1, side view.
30S ribosomal protein S4, chloroplastic in PDB entry 8ip9, assembly 1, top view.
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S5 DRBM domain-containing protein
Chain: fb
Length: 274 amino acids
Theoretical weight: 30 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6LVN2 (Residues: 1-274; Coverage: 100%)
Pfam:
S5 DRBM domain-containing protein in PDB entry 8ip9, assembly 1, front view.
S5 DRBM domain-containing protein in PDB entry 8ip9, assembly 1, side view.
S5 DRBM domain-containing protein in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S6
Chain: gb
Length: 250 amino acids
Theoretical weight: 28.49 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A2X0SLI3 (Residues: 1-250; Coverage: 100%)
Pfam: Ribosomal protein S6e
40S ribosomal protein S6 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S6 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S6 in PDB entry 8ip9, assembly 1, top view.
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40S ribosomal protein S7
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
Pfam: Ribosomal protein S7e
40S ribosomal protein S7 in PDB entry 8ip9, assembly 1, front view.
40S ribosomal protein S7 in PDB entry 8ip9, assembly 1, side view.
40S ribosomal protein S7 in PDB entry 8ip9, assembly 1, top view.
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Small ribosomal subunit protein uS17 N-terminal domain-containing protein
Chain: ib
Length: 159 amino acids
Theoretical weight: 17.84 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5BFB7 (Residues: 1-159; Coverage: 100%)
Pfam:
Small ribosomal subunit protein uS17 N-terminal domain-containing protein in PDB entry 8ip9, assembly 1, front view.
Small ribosomal subunit protein uS17 N-terminal domain-containing protein in PDB entry 8ip9, assembly 1, side view.
Small ribosomal subunit protein uS17 N-terminal domain-containing protein in PDB entry 8ip9, assembly 1, top view.
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Small ribosomal subunit protein eS32
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
Pfam: Ribosomal protein L41
Small ribosomal subunit protein eS32 in PDB entry 8ip9, assembly 1, front view.
Small ribosomal subunit protein eS32 in PDB entry 8ip9, assembly 1, side view.
Small ribosomal subunit protein eS32 in PDB entry 8ip9, assembly 1, top view.
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RNA chain aa
Name: 18S Ribosomal RNA
Representative chains: aa
Length: 1810 nucleotides
Theoretical weight: 583.61 KDa
Rfam: Eukaryotic small subunit ribosomal RNA
18S Ribosomal RNA in PDB entry 8ip9, assembly 1, front view.
18S Ribosomal RNA in PDB entry 8ip9, assembly 1, side view.
18S Ribosomal RNA in PDB entry 8ip9, assembly 1, top view.
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RNA chain al
Name: Messenger RNA
Representative chains: al
Length: 7 nucleotides
Theoretical weight: 2.23 KDa
Messenger RNA in PDB entry 8ip9, assembly 1, front view.
Messenger RNA in PDB entry 8ip9, assembly 1, side view.
Messenger RNA in PDB entry 8ip9, assembly 1, top view.
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RNA chain cl
Name: tRNAi
Representative chains: cl
Length: 75 nucleotides
Theoretical weight: 24.45 KDa
Rfam: tRNA
tRNAi in PDB entry 8ip9, assembly 1, front view.
tRNAi in PDB entry 8ip9, assembly 1, side view.
tRNAi in PDB entry 8ip9, assembly 1, top view.
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