› 6yam

Electron Microscopy
3.6Å resolution

Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin mRNA

Released:
DOI: 10.2210/pdb6yam/pdb
PDB entry 6yam coloured by chain, front view.
PDB entry 6yam coloured by chain, side view.
PDB entry 6yam coloured by chain, top view.
Source organism: Oryctolagus cuniculus
Primary publication:
Structural insights into the mammalian late-stage initiation complexes
Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y.
(2019)
Related structures: EMD-10761

Function and Biology Details

Reaction catalysed: 
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 50-mer (preferred)
PDBe Complex ID:
PDB-CPX-100605 (preferred)
Entry contents:
47 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (50 distinct):
Small ribosomal subunit protein eS32 Chain: l
Molecule details ›
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
Sequence domains: Ribosomal protein L41
Small ribosomal subunit protein uS2 Chain: C
Molecule details ›
Chain: C
Length: 208 amino acids
Theoretical weight: 23.36 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TLT8 (Residues: 2-209; Coverage: 71%)
Gene name: RPSA
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS1 Chain: D
Molecule details ›
Chain: D
Length: 264 amino acids
Theoretical weight: 29.93 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TN72 (Residues: 1-264; Coverage: 100%)
Gene name: RPS3A
Sequence domains: Ribosomal S3Ae family
40S ribosomal protein uS5 Chain: E
Molecule details ›
Chain: E
Length: 226 amino acids
Theoretical weight: 24.81 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein uS3 Chain: F
Molecule details ›
Chain: F
Length: 227 amino acids
Theoretical weight: 25.16 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TNM3 (Residues: 39-265; Coverage: 81%)
Gene name: RPS3
Sequence domains:
Small ribosomal subunit protein eS4 Chain: G
Molecule details ›
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
Sequence domains:
Small ribosomal subunit protein uS7 Chain: H
Molecule details ›
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
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein eS6 Chain: I
Molecule details ›
Chain: I
Length: 237 amino acids
Theoretical weight: 27.47 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TM55 (Residues: 11-211; Coverage: 81%)
Gene name: RPS6
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7 Chain: J
Molecule details ›
Chain: J
Length: 190 amino acids
Theoretical weight: 21.72 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SVB0 (Residues: 243-432; Coverage: 44%)
Gene name: RPS7
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8 Chain: K
Molecule details ›
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
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4 Chain: L
Molecule details ›
Chain: L
Length: 182 amino acids
Theoretical weight: 21.27 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: B7NZS8 (Residues: 7-188; Coverage: 94%)
Gene name: RPS9
Sequence domains:
Small ribosomal subunit protein eS10 Chain: M
Molecule details ›
Chain: M
Length: 98 amino acids
Theoretical weight: 11.77 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T168 (Residues: 61-158; Coverage: 44%)
Gene name: RPS10
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein uS17 Chain: N
Molecule details ›
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
Sequence domains:
Small ribosomal subunit protein eS12 Chain: O
Molecule details ›
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
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS15 Chain: P
Molecule details ›
Chain: P
Length: 150 amino acids
Theoretical weight: 17.13 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SP51 (Residues: 11-152; Coverage: 92%)
Gene name: RPS13
Sequence domains:
Small ribosomal subunit protein uS11 Chain: Q
Molecule details ›
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
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS9 Chain: S
Molecule details ›
Chain: S
Length: 141 amino acids
Theoretical weight: 15.98 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SGX4 (Residues: 32-172; Coverage: 82%)
Gene name: RPS16
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein eS17 Chain: T
Molecule details ›
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
Sequence domains: Ribosomal S17
Small ribosomal subunit protein eS19 Chain: V
Molecule details ›
Chain: V
Length: 145 amino acids
Theoretical weight: 16.24 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TN62 (Residues: 1-145; Coverage: 100%)
Gene name: RPS19
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 Chain: W
Molecule details ›
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
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein eS21 Chain: X
Molecule details ›
Chain: X
Length: 82 amino acids
Theoretical weight: 8.9 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TM82 (Residues: 24-80; Coverage: 51%)
Gene name: RPS21
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein uS8 Chain: Y
Molecule details ›
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
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS12 Chain: Z
Molecule details ›
Chain: Z
Length: 142 amino acids
Theoretical weight: 15.76 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SZ47 (Residues: 1-142; Coverage: 99%)
Gene name: RPS23
Sequence domains: Ribosomal protein S12/S23
40S ribosomal protein S24 Chain: a
Molecule details ›
Chain: a
Length: 133 amino acids
Theoretical weight: 15.43 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TS40 (Residues: 1-133; Coverage: 100%)
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS26 Chain: b
Molecule details ›
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
Sequence domains: Ribosomal protein S26e
Small ribosomal subunit protein eS27 Chain: c
Molecule details ›
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
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS28 Chain: d
Molecule details ›
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
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein uS14 Chain: e
Molecule details ›
Chain: e
Length: 53 amino acids
Theoretical weight: 6.36 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U7M4 (Residues: 4-56; Coverage: 95%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein eS31 Chain: f
Molecule details ›
Chain: f
Length: 71 amino acids
Theoretical weight: 8.36 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SK22 (Residues: 114-184; Coverage: 38%)
Gene name: RPS27A
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein RACK1 Chain: g
Molecule details ›
Chain: g
Length: 313 amino acids
Theoretical weight: 34.67 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SJB4 (Residues: 117-421; Coverage: 72%)
Gene name: RACK1
Sequence domains: WD domain, G-beta repeat
Small ribosomal subunit protein eS25 Chain: n
Molecule details ›
Chain: n
Length: 75 amino acids
Theoretical weight: 8.53 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TDB3 (Residues: 40-114; Coverage: 61%)
Gene name: RPS25
Sequence domains: S25 ribosomal protein
Small ribosomal subunit protein eS30 Chain: i
Molecule details ›
Chain: i
Length: 59 amino acids
Theoretical weight: 6.74 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T8A2 (Residues: 75-133; Coverage: 44%)
Gene name: FAU
Sequence domains: Ribosomal protein S30
Eukaryotic translation initiation factor 2 subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 266 amino acids
Theoretical weight: 30.63 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T2G4 (Residues: 6-271; Coverage: 94%)
Gene name: EIF2S1
Sequence domains:
eukaryotic translation initiation factor 2 subunit gamma Chain: B
Molecule details ›
Chain: B
Length: 422 amino acids
Theoretical weight: 45.86 KDa
Source organism: Oryctolagus cuniculus
eukaryotic translation initiation factor 1A Chain: j
Molecule details ›
Chain: j
Length: 144 amino acids
Theoretical weight: 16.49 KDa
Source organism: Oryctolagus cuniculus
ATP-binding cassette sub-family E member 1 (ABCE1) Chain: k
Molecule details ›
Chain: k
Length: 595 amino acids
Theoretical weight: 66.99 KDa
Source organism: Oryctolagus cuniculus
Small ribosomal subunit protein uS13 Chain: U
Molecule details ›
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
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS19 Chain: R
Molecule details ›
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
Sequence domains: Ribosomal protein S19
eukaryotic translation initiation factor 3 subunit d Chain: m
Molecule details ›
Chain: m
Length: 548 amino acids
Theoretical weight: 64.04 KDa
Source organism: Oryctolagus cuniculus
Eukaryotic translation initiation factor 3 subunit A Chain: y
Molecule details ›
Chain: y
Length: 1350 amino acids
Theoretical weight: 163.23 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A5F9C991 (Residues: 1-1350; Coverage: 100%)
Gene names: EIF3A, EIF3S10
Sequence domains: PCI domain
Eukaryotic translation initiation factor 3 subunit C Chain: v
Molecule details ›
Chain: v
Length: 913 amino acids
Theoretical weight: 105.68 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U971 (Residues: 1-913; Coverage: 100%)
Gene names: EIF3C, EIF3S8
Sequence domains:
Eukaryotic translation initiation factor 3 subunit E Chain: w
Molecule details ›
Chain: w
Length: 445 amino acids
Theoretical weight: 52.28 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SUC8 (Residues: 18-462; Coverage: 96%)
Gene names: EIF3E, EIF3S6, INT6
Sequence domains:
Eukaryotic translation initiation factor 3 subunit F Chain: q
Molecule details ›
Chain: q
Length: 272 amino acids
Theoretical weight: 30.11 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SLC2 (Residues: 93-364; Coverage: 75%)
Gene names: EIF3F, EIF3S5
Sequence domains:
eukaryotic translation initiation factor 3 subunit h Chain: r
Molecule details ›
Chain: r
Length: 352 amino acids
Theoretical weight: 39.95 KDa
Source organism: Oryctolagus cuniculus
Eukaryotic translation initiation factor 3 subunit K Chain: s
Molecule details ›
Chain: s
Length: 218 amino acids
Theoretical weight: 25.13 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T3L2 (Residues: 1-218; Coverage: 100%)
Gene names: EIF3K, EIF3S12
Sequence domains: CSN8/PSMD8/EIF3K family
eukaryotic translation initiation factor 3 subunit l Chain: t
Molecule details ›
Chain: t
Length: 564 amino acids
Theoretical weight: 66.78 KDa
Source organism: Oryctolagus cuniculus
Eukaryotic translation initiation factor 3 subunit M Chain: u
Molecule details ›
Chain: u
Length: 374 amino acids
Theoretical weight: 42.56 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SLW8 (Residues: 1-374; Coverage: 100%)
Gene name: EIF3M
Sequence domains:
initiator methionylated tRNA Chain: 1
Molecule details ›
Chain: 1
Length: 75 nucleotides
Theoretical weight: 24.38 KDa
Sequence domains: tRNA
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1863 nucleotides
Theoretical weight: 601.02 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
beta-globin mRNA Chain: 3
Molecule details ›
Chain: 3
Length: 45 nucleotides
Theoretical weight: 14.45 KDa

Ligands and Environments

3 bound ligands:
Ligand SF4 2 x SF4
Ligand MG 1 x MG
Ligand GNP 2 x GNP
1 modified residue:
Ligand T6A 1 x T6A

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-10761

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