8PJ2 image
Entry Detail
PDB ID:
8PJ2
EMDB ID:
Keywords:
Title:
Structure of human 48S translation initiation complex in AUG recognition state after eIF5-induced GTP hydrolysis by eIF2 (48S-2)
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2023-06-22
Release Date:
2024-08-14
Method Details:
Experimental Method:
Resolution:
3.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit B
Chain IDs:A (auth: 1)
Chain Length:814
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit I
Chain IDs:B (auth: 2)
Chain Length:325
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit K
Chain IDs:C (auth: 3)
Chain Length:218
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit F
Chain IDs:D (auth: 4)
Chain Length:357
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit L
Chain IDs:E (auth: 5)
Chain Length:564
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit M
Chain IDs:F (auth: 6)
Chain Length:374
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:G (auth: 7)
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit H
Chain IDs:H (auth: 8)
Chain Length:352
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L41
Chain IDs:I (auth: 9)
Chain Length:25
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:18S rRNA
Chain IDs:J (auth: A)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S11
Chain IDs:K (auth: B)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S4, X isoform
Chain IDs:L (auth: C)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S9
Chain IDs:M (auth: D)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S23
Chain IDs:N (auth: E)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S30
Chain IDs:O (auth: F)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S7
Chain IDs:P (auth: G)
Chain Length:194
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27
Chain IDs:Q (auth: H)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S13
Chain IDs:R (auth: I)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15a
Chain IDs:S (auth: J)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S21
Chain IDs:T (auth: K)
Chain Length:83
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S2
Chain IDs:U (auth: L)
Chain Length:293
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S17
Chain IDs:V (auth: M)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein SA
Chain IDs:W (auth: N)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3a
Chain IDs:X (auth: O)
Chain Length:320
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S14
Chain IDs:Y (auth: P)
Chain Length:151
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S26
Chain IDs:Z (auth: Q)
Chain Length:144
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8
Chain IDs:AA (auth: R)
Chain Length:315
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S6
Chain IDs:BA (auth: S)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24
Chain IDs:CA (auth: T)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S5
Chain IDs:DA (auth: V)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S16
Chain IDs:EA (auth: Y)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3
Chain IDs:FA (auth: Z)
Chain Length:243
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S10
Chain IDs:GA (auth: a)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15
Chain IDs:HA (auth: b)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Receptor of activated protein C kinase 1
Chain IDs:IA (auth: c)
Chain Length:263
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S19
Chain IDs:JA (auth: d)
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25
Chain IDs:KA (auth: e)
Chain Length:143
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S18
Chain IDs:LA (auth: f)
Chain Length:59
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S20
Chain IDs:MA (auth: h)
Chain Length:84
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S29
Chain IDs:NA (auth: i)
Chain Length:56
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Ubiquitin
Chain IDs:OA (auth: k)
Chain Length:83
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S12
Chain IDs:PA (auth: m)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S28
Chain IDs:QA (auth: n)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit G
Chain IDs:RA (auth: o)
Chain Length:320
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 1A, X-chromosomal
Chain IDs:SA (auth: q)
Chain Length:144
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 2 subunit 1
Chain IDs:TA (auth: r)
Chain Length:315
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 2 subunit 3
Chain IDs:UA (auth: t)
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit A
Chain IDs:VA (auth: u)
Chain Length:1382
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit E
Chain IDs:WA (auth: v)
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:Initiator Met-tRNA-i
Chain IDs:XA (auth: w)
Chain Length:75
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit D
Chain IDs:YA (auth: x)
Chain Length:548
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 3 subunit C
Chain IDs:ZA (auth: y)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 5
Chain IDs:AB (auth: z)
Chain Length:243
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5MC J C modified residue
5MU J U modified residue
6MZ J A modified residue
A2M J A modified residue
JMH J C modified residue
MA6 J A modified residue
OMC J C modified residue
OMG J G modified residue
OMU J U modified residue
PSU J U modified residue
UR3 J U modified residue
Primary Citation
Structural basis for translational control by the human 48S initiation complex.
Nat.Struct.Mol.Biol. ? ? ? (2024)
PMID: 39289545 DOI: 10.1038/s41594-024-01378-4

Abstact

The selection of an open reading frame (ORF) for translation of eukaryotic mRNA relies on remodeling of the scanning 48S initiation complex into an elongation-ready 80S ribosome. Using cryo-electron microscopy, we visualize the key commitment steps orchestrating 48S remodeling in humans. The mRNA Kozak sequence facilitates mRNA scanning in the 48S open state and stabilizes the 48S closed state by organizing the contacts of eukaryotic initiation factors (eIFs) and ribosomal proteins and by reconfiguring mRNA structure. GTPase-triggered large-scale fluctuations of 48S-bound eIF2 facilitate eIF5B recruitment, transfer of initiator tRNA from eIF2 to eIF5B and the release of eIF5 and eIF2. The 48S-bound multisubunit eIF3 complex controls ribosomal subunit joining by coupling eIF exchange to gradual displacement of the eIF3c N-terminal domain from the intersubunit interface. These findings reveal the structural mechanism of ORF selection in human cells and explain how eIF3 could function in the context of the 80S ribosome.

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Primary Citation of related structures