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48S late-stage initiation complex with m6A mRNA

Electron Microscopy
3.04Å resolution
PDB entry 8p03 coloured by chain, front view.
PDB entry 8p03 coloured by chain, side view.
PDB entry 8p03 coloured by chain, top view.
Source organism: Oryctolagus cuniculus
Assembly composition:
hetero 40-mer (preferred)
Entry contents: 37 distinct polypeptide molecules
3 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 40-mer
Accessible surface area: 469443.75 Å2
Buried surface area: 228120.72 Å2
Dissociation area: 1,920.32 Å2
Dissociation energy (ΔGdiss): 6.31 kcal/mol
Dissociation entropy (TΔSdiss): 11.66 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-268545

Macromolecules

Eukaryotic translation initiation factor 2 subunit 1
Chain: A
Length: 284 amino acids
Theoretical weight: 32.79 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T2G4 (Residues: 1-284; Coverage: 100%)
Gene name: EIF2S1
Pfam:
Eukaryotic translation initiation factor 2 subunit 1 in PDB entry 8p03, assembly 1, front view.
Eukaryotic translation initiation factor 2 subunit 1 in PDB entry 8p03, assembly 1, side view.
Eukaryotic translation initiation factor 2 subunit 1 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS2
Chain: C
Length: 207 amino acids
Theoretical weight: 23.27 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TLT8 (Residues: 3-209; Coverage: 70%)
Gene name: RPSA
Pfam: Ribosomal protein S2
Small ribosomal subunit protein uS2 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS2 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS2 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS1
Chain: D
Length: 215 amino acids
Theoretical weight: 24.94 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TN72 (Residues: 19-233; Coverage: 81%)
Gene name: RPS3A
Pfam: Ribosomal S3Ae family
Small ribosomal subunit protein eS1 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS1 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS1 in PDB entry 8p03, assembly 1, top view.
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40S ribosomal protein S2
Chain: E
Length: 270 amino acids
Theoretical weight: 29.1 KDa
Source organism: Oryctolagus cuniculus
40S ribosomal protein S2 in PDB entry 8p03, assembly 1, front view.
40S ribosomal protein S2 in PDB entry 8p03, assembly 1, side view.
40S ribosomal protein S2 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS3
Chain: F
Length: 227 amino acids
Theoretical weight: 25.16 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TNM3 (Residues: 1-227; Coverage: 93%)
Gene name: RPS3
Pfam:
Small ribosomal subunit protein uS3 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS3 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS3 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS4
Chain: G
Length: 263 amino acids
Theoretical weight: 29.66 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TK17 (Residues: 1-263; Coverage: 100%)
Gene name: RPS4X
Pfam:
Small ribosomal subunit protein eS4 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS4 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS4 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS7
Chain: H
Length: 191 amino acids
Theoretical weight: 21.53 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: U3KMN4 (Residues: 29-219; Coverage: 87%)
Gene name: RPS5
Pfam: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS7 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS7 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS7 in PDB entry 8p03, assembly 1, top view.
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40S ribosomal protein S6
Chain: I
Length: 237 amino acids
Theoretical weight: 27.48 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A5K1UJS7 (Residues: 1-237; Coverage: 95%)
Pfam: Ribosomal protein S6e
40S ribosomal protein S6 in PDB entry 8p03, assembly 1, front view.
40S ribosomal protein S6 in PDB entry 8p03, assembly 1, side view.
40S ribosomal protein S6 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS7
Chain: J
Length: 190 amino acids
Theoretical weight: 21.72 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SVB0 (Residues: 5-194; Coverage: 98%)
Gene name: RPS7
Small ribosomal subunit protein eS7 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS7 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS7 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS8
Chain: K
Length: 206 amino acids
Theoretical weight: 23.9 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TJW1 (Residues: 2-207; Coverage: 99%)
Gene name: RPS8
Pfam: Ribosomal protein S8e
Small ribosomal subunit protein eS8 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS8 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS8 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS4
Chain: L
Length: 194 amino acids
Theoretical weight: 22.64 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: B7NZS8 (Residues: 1-194; Coverage: 100%)
Gene name: RPS9
Pfam:
Small ribosomal subunit protein uS4 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS4 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS4 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS10
Chain: M
Length: 98 amino acids
Theoretical weight: 11.77 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TPV3 (Residues: 1-98; Coverage: 59%)
Pfam: Plectin/S10 domain
Small ribosomal subunit protein eS10 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS10 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS10 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS17
Chain: N
Length: 158 amino acids
Theoretical weight: 18.47 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TRM4 (Residues: 1-158; Coverage: 100%)
Gene name: RPS11
Pfam:
Small ribosomal subunit protein uS17 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS17 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS17 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS12
Chain: O
Length: 132 amino acids
Theoretical weight: 14.54 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SFR8 (Residues: 1-132; Coverage: 100%)
Gene name: RPS12
Pfam: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein eS12 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS12 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS12 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS15
Chain: P
Length: 150 amino acids
Theoretical weight: 17.13 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SP51 (Residues: 2-151; Coverage: 99%)
Gene name: RPS13
Pfam:
Small ribosomal subunit protein uS15 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS15 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS15 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS11
Chain: Q
Length: 151 amino acids
Theoretical weight: 16.3 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T1F0 (Residues: 1-151; Coverage: 100%)
Gene name: RPS14
Pfam: Ribosomal protein S11
Small ribosomal subunit protein uS11 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS11 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS11 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS19
Chain: R
Length: 145 amino acids
Theoretical weight: 17.05 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U0Q2 (Residues: 1-145; Coverage: 100%)
Gene name: RPS15
Pfam: Ribosomal protein S19
Small ribosomal subunit protein uS19 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS19 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS19 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS9
Chain: S
Length: 141 amino acids
Theoretical weight: 15.98 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SGX4 (Residues: 6-146; Coverage: 97%)
Gene name: RPS16
Pfam: Ribosomal protein S9/S16
Small ribosomal subunit protein uS9 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS9 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS9 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS17
Chain: T
Length: 135 amino acids
Theoretical weight: 15.55 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TU13 (Residues: 1-135; Coverage: 100%)
Gene name: RPS17
Pfam: Ribosomal S17
Small ribosomal subunit protein eS17 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS17 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS17 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS13
Chain: U
Length: 152 amino acids
Theoretical weight: 17.76 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TPG3 (Residues: 1-152; Coverage: 100%)
Gene name: RPS18
Pfam: Ribosomal protein S13/S18
Small ribosomal subunit protein uS13 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS13 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS13 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS19
Chain: V
Length: 141 amino acids
Theoretical weight: 15.81 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TN62 (Residues: 4-144; Coverage: 97%)
Gene name: RPS19
Pfam: Ribosomal protein S19e
Small ribosomal subunit protein eS19 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS19 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS19 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS10
Chain: W
Length: 119 amino acids
Theoretical weight: 13.4 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SIZ2 (Residues: 1-119; Coverage: 100%)
Gene name: RPS20
Pfam: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS10 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS10 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS10 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS21
Chain: X
Length: 83 amino acids
Theoretical weight: 9.12 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: Q32PB8 (Residues: 1-83; Coverage: 100%)
Gene name: RPS21
Pfam: Ribosomal protein S21e
Small ribosomal subunit protein eS21 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS21 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS21 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS8
Chain: Y
Length: 130 amino acids
Theoretical weight: 14.87 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TG89 (Residues: 1-130; Coverage: 100%)
Gene name: RPS15A
Pfam: Ribosomal protein S8
Small ribosomal subunit protein uS8 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS8 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS8 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS12
Chain: Z
Length: 143 amino acids
Theoretical weight: 15.84 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SZ47 (Residues: 1-143; Coverage: 100%)
Gene name: RPS23
Pfam: Ribosomal protein S12/S23
Small ribosomal subunit protein uS12 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS12 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS12 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS24
Chain: a
Length: 133 amino acids
Theoretical weight: 15.43 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A5F9D2E6 (Residues: 1-133; Coverage: 100%)
Gene name: RPS24
Pfam: Ribosomal protein S24e
Small ribosomal subunit protein eS24 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS24 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS24 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS26
Chain: b
Length: 115 amino acids
Theoretical weight: 12.96 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TFE8 (Residues: 1-115; Coverage: 100%)
Gene name: RPS26
Pfam: Ribosomal protein S26e
Small ribosomal subunit protein eS26 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS26 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS26 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS27
Chain: c
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TZ76 (Residues: 1-84; Coverage: 100%)
Gene name: RPS27
Pfam: Ribosomal protein S27
Small ribosomal subunit protein eS27 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS27 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS27 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS28
Chain: d
Length: 69 amino acids
Theoretical weight: 7.86 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TIB4 (Residues: 1-69; Coverage: 100%)
Gene name: RPS28
Pfam: Ribosomal protein S28e
Small ribosomal subunit protein eS28 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS28 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS28 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein uS14
Chain: e
Length: 56 amino acids
Theoretical weight: 6.69 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U7M4 (Residues: 1-56; Coverage: 100%)
Gene name: RPS29
Pfam: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS14 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein uS14 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein uS14 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS31
Chain: f
Length: 71 amino acids
Theoretical weight: 8.36 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SK22 (Residues: 82-152; Coverage: 46%)
Gene name: RPS27A
Pfam:
Small ribosomal subunit protein eS31 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS31 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS31 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein RACK1
Chain: g
Length: 313 amino acids
Theoretical weight: 34.67 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SJB4 (Residues: 2-314; Coverage: 99%)
Gene name: RACK1
Pfam: WD domain, G-beta repeat
Small ribosomal subunit protein RACK1 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein RACK1 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein RACK1 in PDB entry 8p03, assembly 1, top view.
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Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
Chain: i
Length: 133 amino acids
Theoretical weight: 14.5 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T8A2 (Residues: 1-133; Coverage: 100%)
Gene name: FAU
Pfam:
Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein in PDB entry 8p03, assembly 1, front view.
Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein in PDB entry 8p03, assembly 1, side view.
Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein in PDB entry 8p03, assembly 1, top view.
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Eukaryotic translation initiation factor 4C
Chain: j
Length: 111 amino acids
Theoretical weight: 12.79 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SYS4 (Residues: 5-115; Coverage: 77%)
Pfam: Translation initiation factor 1A / IF-1
Eukaryotic translation initiation factor 4C in PDB entry 8p03, assembly 1, front view.
Eukaryotic translation initiation factor 4C in PDB entry 8p03, assembly 1, side view.
Eukaryotic translation initiation factor 4C in PDB entry 8p03, assembly 1, top view.
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ATP binding cassette subfamily E member 1
Chain: k
Length: 595 amino acids
Theoretical weight: 66.99 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SG72 (Residues: 4-598; Coverage: 99%)
Pfam:
ATP binding cassette subfamily E member 1 in PDB entry 8p03, assembly 1, front view.
ATP binding cassette subfamily E member 1 in PDB entry 8p03, assembly 1, side view.
ATP binding cassette subfamily E member 1 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS32
Chain: l
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A087WNH4 (Residues: 1-25; Coverage: 100%)
Gene name: RPL41
Pfam: Ribosomal protein L41
Small ribosomal subunit protein eS32 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS32 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS32 in PDB entry 8p03, assembly 1, top view.
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Small ribosomal subunit protein eS25
Chain: n
Length: 124 amino acids
Theoretical weight: 13.65 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TDB3 (Residues: 1-124; Coverage: 100%)
Gene name: RPS25
Pfam: S25 ribosomal protein
Small ribosomal subunit protein eS25 in PDB entry 8p03, assembly 1, front view.
Small ribosomal subunit protein eS25 in PDB entry 8p03, assembly 1, side view.
Small ribosomal subunit protein eS25 in PDB entry 8p03, assembly 1, top view.
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RNA chain 1
Name: initiator methionylated tRNA
Representative chains: 1
Length: 75 nucleotides
Theoretical weight: 24.38 KDa
Rfam: tRNA
initiator methionylated tRNA in PDB entry 8p03, assembly 1, front view.
initiator methionylated tRNA in PDB entry 8p03, assembly 1, side view.
initiator methionylated tRNA in PDB entry 8p03, assembly 1, top view.
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RNA chain 2
Name: 18S Ribosomal RNA
Representative chains: 2
Length: 1863 nucleotides
Theoretical weight: 601.02 KDa
Rfam: Eukaryotic small subunit ribosomal RNA
18S Ribosomal RNA in PDB entry 8p03, assembly 1, front view.
18S Ribosomal RNA in PDB entry 8p03, assembly 1, side view.
18S Ribosomal RNA in PDB entry 8p03, assembly 1, top view.
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RNA chain 3
Name: m6A-methylated mRNA
Representative chains: 3
Length: 9 nucleotides
Theoretical weight: 2.88 KDa
m6A-methylated mRNA in PDB entry 8p03, assembly 1, front view.
m6A-methylated mRNA in PDB entry 8p03, assembly 1, side view.
m6A-methylated mRNA in PDB entry 8p03, assembly 1, top view.
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