7SYV image
Entry Detail
PDB ID:
7SYV
EMDB ID:
Keywords:
Title:
Structure of the wt IRES eIF5B-containing pre-48S initiation complex, open conformation. Structure 14(wt)
Biological Source:
PDB Version:
Deposition Date:
2021-11-25
Release Date:
2022-07-20
Method Details:
Experimental Method:
Resolution:
3.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:18S rRNA
Chain IDs:A (auth: 2)
Chain Length:1870
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 1A, X-chromosomal
Chain IDs:C (auth: A)
Chain Length:144
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:40S ribosomal protein SA
Chain IDs:E (auth: B)
Chain Length:295
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS1
Chain IDs:G (auth: C)
Chain Length:264
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S2
Chain IDs:I (auth: D)
Chain Length:221
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS3
Chain IDs:K (auth: E)
Chain Length:56
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S4
Chain IDs:M (auth: F)
Chain Length:263
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS7
Chain IDs:O (auth: G)
Chain Length:204
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS6
Chain IDs:Q (auth: H)
Chain Length:317
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S7
Chain IDs:S (auth: I)
Chain Length:432
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS8
Chain IDs:U (auth: J)
Chain Length:208
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS4
Chain IDs:W (auth: K)
Chain Length:194
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS10
Chain IDs:Y (auth: L)
Chain Length:149
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS17
Chain IDs:AA (auth: M)
Chain Length:158
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS12
Chain IDs:BA (auth: N)
Chain Length:25
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS15
Chain IDs:CA (auth: O)
Chain Length:151
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS11
Chain IDs:DA (auth: P)
Chain Length:168
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS19
Chain IDs:EA (auth: Q)
Chain Length:145
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS9
Chain IDs:FA (auth: R)
Chain Length:172
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS17
Chain IDs:GA (auth: S)
Chain Length:135
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS13
Chain IDs:HA (auth: T)
Chain Length:152
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS19
Chain IDs:IA (auth: U)
Chain Length:145
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS10
Chain IDs:JA (auth: V)
Chain Length:119
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S21
Chain IDs:KA (auth: W)
Chain Length:83
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS8
Chain IDs:LA (auth: X)
Chain Length:627
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:uS12
Chain IDs:MA (auth: Y)
Chain Length:143
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24
Chain IDs:B (auth: Z)
Chain Length:400
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25
Chain IDs:D (auth: a)
Chain Length:144
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS26
Chain IDs:F (auth: b)
Chain Length:295
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS27
Chain IDs:H (auth: c)
Chain Length:264
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS28
Chain IDs:J (auth: d)
Chain Length:221
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS29
Chain IDs:L (auth: e)
Chain Length:56
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:eS30
Chain IDs:N (auth: f)
Chain Length:263
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27a
Chain IDs:P (auth: g)
Chain Length:204
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:RACK1
Chain IDs:R (auth: h)
Chain Length:317
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Description:Met-tRNA-i-Met
Chain IDs:T (auth: i)
Chain Length:432
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:60s ribosomal protein l41
Chain IDs:V (auth: n)
Chain Length:25
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Description:Eukaryotic translation initiation factor 5B
Chain IDs:X (auth: x)
Chain Length:627
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Description:HCV IRES
Chain IDs:Z (auth: z)
Chain Length:400
Number of Molecules:1
Biological Source:hepatitis C virus genotype 1a
Primary Citation
Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES.
Embo J. 41 e110581 e110581 (2022)
PMID: 35822879 DOI: 10.15252/embj.2022110581

Abstact

Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical studies revealed that direct binding of the IRES to the 40S ribosomal subunit places the initiation codon into the P site, where it base pairs with eIF2-bound Met-tRNAiMet forming a 48S initiation complex. Subsequently, eIF5 and eIF5B mediate subunit joining, yielding an elongation-competent 80S ribosome. Initiation can also proceed without eIF2, in which case Met-tRNAiMet is recruited directly by eIF5B. However, the structures of initiation complexes assembled on the HCV IRES, the transitions between different states, and the accompanying conformational changes have remained unknown. To fill these gaps, we now obtained cryo-EM structures of IRES initiation complexes, at resolutions up to 3.5 Å, that cover all major stages from the initial ribosomal association, through eIF2-containing 48S initiation complexes, to eIF5B-containing complexes immediately prior to subunit joining. These structures provide insights into the dynamic network of 40S/IRES contacts, highlight the role of IRES domain II, and reveal conformational changes that occur during the transition from eIF2- to eIF5B-containing 48S complexes and prepare them for subunit joining.

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