6YAN

Mammalian 48S late-stage translation initiation complex with histone 4 mRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Insights into the Mammalian Late-Stage Initiation Complexes.

Simonetti, A.Guca, E.Bochler, A.Kuhn, L.Hashem, Y.

(2020) Cell Rep 31: 107497-107497

  • DOI: 10.1016/j.celrep.2020.03.061
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role r ...

    In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.


    Organizational Affiliation

    INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France. Electronic address: yaser.hashem@u-bordeaux.fr.



Macromolecules

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4G263Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100338112
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S11N158Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS15P150Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS11Q136Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS14
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24a126Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TS40 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS25h75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 2 subunit 1A266Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF2S1
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS13U142Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
60s ribosomal protein l41l25Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8K206Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100352057
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S9 (Predicted)L182Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS10M98Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348511
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12O124Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS9S141Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS16
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS17T126Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353606RPS17
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS19V141Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345774
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SAC208Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSALOC100144340
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal_S10 domain-containing proteinW104Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS20LOC100341365LOC100348955LOC100354063
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21X82Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS21
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S15aY129Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS12Z142Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS23
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS26b99Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100346996
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27c84Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345694LOC100345044LOC100348261RPS27
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS28d64Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS14e53Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS31f71Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS1D215Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
Find proteins for G1TN72 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein RACK1g313Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS30i59Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
eukaryotic translation initiation factor 2 subunit gammaB422Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S15R135Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS5E226Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TUT9 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S3F227Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S5H191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6I237Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS6
Find proteins for A0A5K1UJS7 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS7J190Oryctolagus cuniculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 33
MoleculeChainsLengthOrganism
18S ribosomal RNA21863Oryctolagus cuniculus

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Entity ID: 34
MoleculeChainsLengthOrganism
histone 4 (H4) mRNA336Mus musculus

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Entity ID: 39
MoleculeChainsLengthOrganism
initiator methionylated tRNA175Oryctolagus cuniculus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union759120
French National Research AgencyFranceANR-14-ACHN-0024

Revision History 

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references