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28S mammalian mitochondrial small ribosomal subunit with mtRF1 and P-site tRNA

Electron Microscopy
3.6Å resolution
PDB entry 8oip coloured by chain, front view.
PDB entry 8oip coloured by chain, side view.
PDB entry 8oip coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 36-mer (preferred)
Entry contents: 33 distinct polypeptide molecules
3 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 36-mer
Accessible surface area: 406443.19 Å2
Buried surface area: 226817.16 Å2
Dissociation area: 484.45 Å2
Dissociation energy (ΔGdiss): -0.68 kcal/mol
Dissociation entropy (TΔSdiss): 8.19 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-236633

Macromolecules

Large ribosomal subunit protein bL19m
Chain: BX
Length: 303 amino acids
Theoretical weight: 34.53 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LNJ0 (Residues: 1-303; Coverage: 100%)
Gene name: MRPL19
Pfam: Ribosomal protein L19
Large ribosomal subunit protein bL19m in PDB entry 8oip, assembly 1, front view.
Large ribosomal subunit protein bL19m in PDB entry 8oip, assembly 1, side view.
Large ribosomal subunit protein bL19m in PDB entry 8oip, assembly 1, top view.
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Mitochondrial ribosomal protein L55
Chain: Bd
Length: 126 amino acids
Theoretical weight: 15.16 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1ULI6 (Residues: 1-126; Coverage: 100%)
Gene name: MRPL55
Pfam: Mitochondrial ribosomal protein L55
Mitochondrial ribosomal protein L55 in PDB entry 8oip, assembly 1, front view.
Mitochondrial ribosomal protein L55 in PDB entry 8oip, assembly 1, side view.
Mitochondrial ribosomal protein L55 in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein
Chain: AB
Length: 366 amino acids
Theoretical weight: 41.36 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SG95 (Residues: 1-366; Coverage: 100%)
Gene name: MRPS35
Pfam: Mitochondrial ribosomal subunit protein
Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein in PDB entry 8oip, assembly 1, top view.
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28S ribosomal protein S24, mitochondrial
Chain: AC
Length: 167 amino acids
Theoretical weight: 18.94 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ANU4 (Residues: 1-167; Coverage: 100%)
Gene name: MRPS24
Pfam: Mitochondrial ribosome subunit S24
28S ribosomal protein S24, mitochondrial in PDB entry 8oip, assembly 1, front view.
28S ribosomal protein S24, mitochondrial in PDB entry 8oip, assembly 1, side view.
28S ribosomal protein S24, mitochondrial in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein mS38
Chain: AD
Length: 199 amino acids
Theoretical weight: 22.84 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D2A802 (Residues: 1-199; Coverage: 100%)
Gene name: AURKAIP1
Pfam: Mitochondrial mRNA-processing protein COX24, C-terminal
Small ribosomal subunit protein mS38 in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein mS38 in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein mS38 in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein bS6m
Chain: AE
Length: 376 amino acids
Theoretical weight: 41.09 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TSM9 (Residues: 28-275; Coverage: 90%)
Pfam: Ribosomal protein S6
Small ribosomal subunit protein bS6m in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein bS6m in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein bS6m in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein uS7m
Chain: AF
Length: 242 amino acids
Theoretical weight: 28.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZJ25 (Residues: 1-242; Coverage: 100%)
Gene name: MRPS7
Pfam: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS7m in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein uS7m in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein uS7m in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein uS10m
Chain: AH
Length: 200 amino acids
Theoretical weight: 23.11 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RUU2 (Residues: 1-200; Coverage: 100%)
Gene name: MRPS10
Pfam: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS10m in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein uS10m in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein uS10m in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein uS12m
Chain: AJ
Length: 139 amino acids
Theoretical weight: 15.26 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL52 (Residues: 1-139; Coverage: 100%)
Pfam: Ribosomal protein S12/S23
Small ribosomal subunit protein uS12m in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein uS12m in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein uS12m in PDB entry 8oip, assembly 1, top view.
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Mitoribosomal protein us14m, mrps14
Chain: AK
Length: 128 amino acids
Theoretical weight: 15.12 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL53 (Residues: 1-128; Coverage: 100%)
Gene name: MRPS14
Pfam: Ribosomal protein S14p/S29e
28S ribosomal protein S14, mitochondrial in PDB entry 8oip, assembly 1, front view.
28S ribosomal protein S14, mitochondrial in PDB entry 8oip, assembly 1, side view.
28S ribosomal protein S14, mitochondrial in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein uS15m
Chain: AL
Length: 259 amino acids
Theoretical weight: 29.6 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AKS1 (Residues: 1-259; Coverage: 100%)
Gene name: MRPS15
Pfam: Ribosomal protein S15
Small ribosomal subunit protein uS15m in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein uS15m in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein uS15m in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein bS16m
Chain: AM
Length: 135 amino acids
Theoretical weight: 15.18 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A480JTD7 (Residues: 1-135; Coverage: 100%)
Pfam: Ribosomal protein S16
Small ribosomal subunit protein bS16m in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein bS16m in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein bS16m in PDB entry 8oip, assembly 1, top view.
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28S ribosomal protein S17, mitochondrial
Chain: AN
Length: 130 amino acids
Theoretical weight: 14.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1UDM1 (Residues: 1-130; Coverage: 100%)
Gene name: MRPS17
Pfam: Ribosomal protein S17
28S ribosomal protein S17, mitochondrial in PDB entry 8oip, assembly 1, front view.
28S ribosomal protein S17, mitochondrial in PDB entry 8oip, assembly 1, side view.
28S ribosomal protein S17, mitochondrial in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein mS40
Chain: AO
Length: 258 amino acids
Theoretical weight: 29.22 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q767K8 (Residues: 1-258; Coverage: 100%)
Gene name: MRPS18B
Pfam: Ribosomal protein S18
Small ribosomal subunit protein mS40 in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein mS40 in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein mS40 in PDB entry 8oip, assembly 1, top view.
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Mitoribosomal protein bs18m, mrps18c
Chain: AP
Length: 143 amino acids
Theoretical weight: 16.21 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL54 (Residues: 1-143; Coverage: 100%)
Gene name: MRPS18C
Pfam: Ribosomal protein S18
28S ribosomal protein S18c, mitochondrial isoform 1 in PDB entry 8oip, assembly 1, front view.
28S ribosomal protein S18c, mitochondrial isoform 1 in PDB entry 8oip, assembly 1, side view.
28S ribosomal protein S18c, mitochondrial isoform 1 in PDB entry 8oip, assembly 1, top view.
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28S ribosomal protein S21, mitochondrial
Chain: AQ
Length: 87 amino acids
Theoretical weight: 10.72 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZNB3 (Residues: 1-87; Coverage: 100%)
Gene name: MRPS21
Pfam: Ribosomal protein S21
28S ribosomal protein S21, mitochondrial in PDB entry 8oip, assembly 1, front view.
28S ribosomal protein S21, mitochondrial in PDB entry 8oip, assembly 1, side view.
28S ribosomal protein S21, mitochondrial in PDB entry 8oip, assembly 1, top view.
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Mitochondrial ribosomal protein S22
Chain: AR
Length: 382 amino acids
Theoretical weight: 43.23 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AQT5 (Residues: 1-382; Coverage: 100%)
Gene name: MRPS22
Pfam: Mitochondrial 28S ribosomal protein S22
Mitochondrial ribosomal protein S22 in PDB entry 8oip, assembly 1, front view.
Mitochondrial ribosomal protein S22 in PDB entry 8oip, assembly 1, side view.
Mitochondrial ribosomal protein S22 in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein mS23 conserved domain-containing protein
Chain: AS
Length: 190 amino acids
Theoretical weight: 21.67 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AEW3 (Residues: 17-207; Coverage: 91%)
Gene name: MRPS23
Pfam: Mitochondrial ribosomal protein S23
Small ribosomal subunit protein mS23 conserved domain-containing protein in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein mS23 conserved domain-containing protein in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein mS23 conserved domain-containing protein in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein mS25
Chain: AT
Length: 173 amino acids
Theoretical weight: 19.95 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL55 (Residues: 1-173; Coverage: 100%)
Gene name: MRPS25
Pfam: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
Small ribosomal subunit protein mS25 in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein mS25 in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein mS25 in PDB entry 8oip, assembly 1, top view.
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Progonadoliberin
Chain: AU
Length: 205 amino acids
Theoretical weight: 23.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AY01 (Residues: 54-77; Coverage: 22%)
Gene name: GNRH2
Progonadoliberin in PDB entry 8oip, assembly 1, front view.
Progonadoliberin in PDB entry 8oip, assembly 1, side view.
Progonadoliberin in PDB entry 8oip, assembly 1, top view.
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Mitochondrial ribosomal protein S27
Chain: AV
Length: 395 amino acids
Theoretical weight: 45.76 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A5G2R1I0 (Residues: 1-395; Coverage: 100%)
Gene name: MRPS27
Pfam: Mitochondrial 28S ribosomal protein S27
Mitochondrial ribosomal protein S27 in PDB entry 8oip, assembly 1, front view.
Mitochondrial ribosomal protein S27 in PDB entry 8oip, assembly 1, side view.
Mitochondrial ribosomal protein S27 in PDB entry 8oip, assembly 1, top view.
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Mitoribosomal protein ms28, mrps28
Chain: AW
Length: 188 amino acids
Theoretical weight: 21.01 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0M3KL56 (Residues: 1-188; Coverage: 100%)
Gene name: MRPS28
Pfam: Mitochondrial ribosomal protein MRP-S35
Mitochondrial ribosomal protein S28 in PDB entry 8oip, assembly 1, front view.
Mitochondrial ribosomal protein S28 in PDB entry 8oip, assembly 1, side view.
Mitochondrial ribosomal protein S28 in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein mS29
Chain: AX
Length: 410 amino acids
Theoretical weight: 46.97 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1XNL0 (Residues: 1-410; Coverage: 100%)
Gene name: DAP3
Pfam: Mitochondrial ribosomal death-associated protein 3
Small ribosomal subunit protein mS29 in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein mS29 in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein mS29 in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein mS31
Chain: AY
Length: 381 amino acids
Theoretical weight: 43.52 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RME2 (Residues: 1-381; Coverage: 100%)
Gene name: MRPS31
Pfam: Mitochondrial 28S ribosomal protein S31
Small ribosomal subunit protein mS31 in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein mS31 in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein mS31 in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein mS33
Chain: AZ
Length: 148 amino acids
Theoretical weight: 16.97 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1V2H3 (Residues: 1-148; Coverage: 100%)
Gene name: MRPS33
Pfam: Mitochondrial ribosomal subunit S27
Small ribosomal subunit protein mS33 in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein mS33 in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein mS33 in PDB entry 8oip, assembly 1, top view.
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Peptide chain release factor 1, mitochondrial
Chain: Aa
Length: 474 amino acids
Theoretical weight: 55.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O75570 (Residues: 1-445; Coverage: 100%)
Gene name: MTRF1
Pfam:
Peptide chain release factor 1, mitochondrial in PDB entry 8oip, assembly 1, front view.
Peptide chain release factor 1, mitochondrial in PDB entry 8oip, assembly 1, side view.
Peptide chain release factor 1, mitochondrial in PDB entry 8oip, assembly 1, top view.
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Mitochondrial ribosomal protein S2
Chain: Ab
Length: 289 amino acids
Theoretical weight: 31.73 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1S001 (Residues: 1-289; Coverage: 100%)
Gene name: MRPS2
Pfam: Ribosomal protein S2
Mitochondrial ribosomal protein S2 in PDB entry 8oip, assembly 1, front view.
Mitochondrial ribosomal protein S2 in PDB entry 8oip, assembly 1, side view.
Mitochondrial ribosomal protein S2 in PDB entry 8oip, assembly 1, top view.
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CHCH domain-containing protein
Chain: Ac
Length: 118 amino acids
Theoretical weight: 13.6 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1SZV4 (Residues: 1-118; Coverage: 100%)
Gene name: CHCHD1
Pfam: CHCH domain
CHCH domain-containing protein in PDB entry 8oip, assembly 1, front view.
CHCH domain-containing protein in PDB entry 8oip, assembly 1, side view.
CHCH domain-containing protein in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein uS5m
Chain: Ad
Length: 430 amino acids
Theoretical weight: 48.21 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SU66 (Residues: 1-430; Coverage: 100%)
Gene name: MRPS5
Pfam:
Small ribosomal subunit protein uS5m in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein uS5m in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein uS5m in PDB entry 8oip, assembly 1, top view.
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Small ribosomal subunit protein mS39
Chain: Ae
Length: 692 amino acids
Theoretical weight: 78.52 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GKS8 (Residues: 1-546, 547-690; Coverage: 100%)
Gene name: PTCD3
Pfam:
Small ribosomal subunit protein mS39 in PDB entry 8oip, assembly 1, front view.
Small ribosomal subunit protein mS39 in PDB entry 8oip, assembly 1, side view.
Small ribosomal subunit protein mS39 in PDB entry 8oip, assembly 1, top view.
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Mitochondrial ribosomal protein S9
Chain: Ag
Length: 397 amino acids
Theoretical weight: 45.6 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LU08 (Residues: 1-397; Coverage: 100%)
Gene name: MRPS9
Pfam: Ribosomal protein S9/S16
Mitochondrial ribosomal protein S9 in PDB entry 8oip, assembly 1, front view.
Mitochondrial ribosomal protein S9 in PDB entry 8oip, assembly 1, side view.
Mitochondrial ribosomal protein S9 in PDB entry 8oip, assembly 1, top view.
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Mitochondrial ribosomal protein S11
Chain: Ai
Length: 196 amino acids
Theoretical weight: 20.86 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZJJ6 (Residues: 1-196; Coverage: 100%)
Gene name: MRPS11
Pfam: Ribosomal protein S11
Mitochondrial ribosomal protein S11 in PDB entry 8oip, assembly 1, front view.
Mitochondrial ribosomal protein S11 in PDB entry 8oip, assembly 1, side view.
Mitochondrial ribosomal protein S11 in PDB entry 8oip, assembly 1, top view.
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Mitochondrial ribosomal protein S34
Chain: Aj
Length: 505 amino acids
Theoretical weight: 55.71 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287AVS9 (Residues: 1-505; Coverage: 100%)
Gene name: MRPS34
Pfam: Mitochondrial 28S ribosomal protein S34
Mitochondrial ribosomal protein S34 in PDB entry 8oip, assembly 1, front view.
Mitochondrial ribosomal protein S34 in PDB entry 8oip, assembly 1, side view.
Mitochondrial ribosomal protein S34 in PDB entry 8oip, assembly 1, top view.
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RNA chain AA
Name: 12S rRNA
Representative chains: AA
Length: 962 nucleotides
Theoretical weight: 309.09 KDa
Rfam: Bacterial small subunit ribosomal RNA
12S rRNA in PDB entry 8oip, assembly 1, front view.
12S rRNA in PDB entry 8oip, assembly 1, side view.
12S rRNA in PDB entry 8oip, assembly 1, top view.
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RNA chain AG
Name: P-site Met-tRNA(fMet)
Representative chains: AG
Length: 72 nucleotides
Theoretical weight: 22.82 KDa
P-site Met-tRNA(fMet) in PDB entry 8oip, assembly 1, front view.
P-site Met-tRNA(fMet) in PDB entry 8oip, assembly 1, side view.
P-site Met-tRNA(fMet) in PDB entry 8oip, assembly 1, top view.
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RNA chain AI
Name: Messenger RNA
Representative chains: AI
Length: 9 nucleotides
Theoretical weight: 2.9 KDa
Messenger RNA in PDB entry 8oip, assembly 1, front view.
Messenger RNA in PDB entry 8oip, assembly 1, side view.
Messenger RNA in PDB entry 8oip, assembly 1, top view.
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