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
  • Primary Citation of Related Structures:  
    6YAN, 6YAM, 6YAL

  • 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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
60s ribosomal protein l41l25Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
Explore A0A087WNH4 
Go to UniProtKB:  A0A087WNH4
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAC208Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSA
Find proteins for G1TLT8 (Oryctolagus cuniculus)
Explore G1TLT8 
Go to UniProtKB:  G1TLT8
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eS1D215Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
Find proteins for G1TN72 (Oryctolagus cuniculus)
Explore G1TN72 
Go to UniProtKB:  G1TN72
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS5E226Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TUT9 (Oryctolagus cuniculus)
Explore G1TUT9 
Go to UniProtKB:  G1TUT9
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S3F227Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
Find proteins for G1TNM3 (Oryctolagus cuniculus)
Explore G1TNM3 
Go to UniProtKB:  G1TNM3
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4G263Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TK17 (Oryctolagus cuniculus)
Explore G1TK17 
Go to UniProtKB:  G1TK17
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S5H191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for G1TFM5 (Oryctolagus cuniculus)
Explore G1TFM5 
Go to UniProtKB:  G1TFM5
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6I237Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A5K1UJS7 (Oryctolagus cuniculus)
Explore A0A5K1UJS7 
Go to UniProtKB:  A0A5K1UJS7
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eS7J190Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SVB0 (Oryctolagus cuniculus)
Explore G1SVB0 
Go to UniProtKB:  G1SVB0
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8K206Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TJW1 (Oryctolagus cuniculus)
Explore G1TJW1 
Go to UniProtKB:  G1TJW1
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S9 (Predicted)L182Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
Find proteins for B7NZS8 (Oryctolagus cuniculus)
Explore B7NZS8 
Go to UniProtKB:  B7NZS8
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS10M98Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TPV3 (Oryctolagus cuniculus)
Explore G1TPV3 
Go to UniProtKB:  G1TPV3
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S11N158Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TRM4 (Oryctolagus cuniculus)
Explore G1TRM4 
Go to UniProtKB:  G1TRM4
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12O124Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
Find proteins for G1SFR8 (Oryctolagus cuniculus)
Explore G1SFR8 
Go to UniProtKB:  G1SFR8
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS11Q136Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T1F0 (Oryctolagus cuniculus)
Explore G1T1F0 
Go to UniProtKB:  G1T1F0
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uS9S141Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SGX4 (Oryctolagus cuniculus)
Explore G1SGX4 
Go to UniProtKB:  G1SGX4
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eS17T126Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TU13 (Oryctolagus cuniculus)
Explore G1TU13 
Go to UniProtKB:  G1TU13
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS19V141Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TN62 (Oryctolagus cuniculus)
Explore G1TN62 
Go to UniProtKB:  G1TN62
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal_S10 domain-containing proteinW104Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
Explore G1SIZ2 
Go to UniProtKB:  G1SIZ2
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21X82Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TM82 (Oryctolagus cuniculus)
Explore G1TM82 
Go to UniProtKB:  G1TM82
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S15aY129Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TG89 (Oryctolagus cuniculus)
Explore G1TG89 
Go to UniProtKB:  G1TG89
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS12Z142Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SZ47 (Oryctolagus cuniculus)
Explore G1SZ47 
Go to UniProtKB:  G1SZ47
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS26b99Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TFE8 (Oryctolagus cuniculus)
Explore G1TFE8 
Go to UniProtKB:  G1TFE8
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27c84Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TZ76 (Oryctolagus cuniculus)
Explore G1TZ76 
Go to UniProtKB:  G1TZ76
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eS28d64Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
Explore G1TIB4 
Go to UniProtKB:  G1TIB4
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uS14e53Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7M4 (Oryctolagus cuniculus)
Explore G1U7M4 
Go to UniProtKB:  G1U7M4
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eS31f71Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
Explore G1SK22 
Go to UniProtKB:  G1SK22
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein RACK1g313Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SJB4 (Oryctolagus cuniculus)
Explore G1SJB4 
Go to UniProtKB:  G1SJB4
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eS25h75Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
Explore G1TDB3 
Go to UniProtKB:  G1TDB3
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS30i59Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T8A2 (Oryctolagus cuniculus)
Explore G1T8A2 
Go to UniProtKB:  G1T8A2
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1A266Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF2S1
Find proteins for G1T2G4 (Oryctolagus cuniculus)
Explore G1T2G4 
Go to UniProtKB:  G1T2G4
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
eukaryotic translation initiation factor 2 subunit gammaB422Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S15R135Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
Explore G1U0Q2 
Go to UniProtKB:  G1U0Q2
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uS15P150Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SP51 (Oryctolagus cuniculus)
Explore G1SP51 
Go to UniProtKB:  G1SP51
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24a126Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TS40 (Oryctolagus cuniculus)
Explore G1TS40 
Go to UniProtKB:  G1TS40
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS13U142Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TPG3 (Oryctolagus cuniculus)
Explore G1TPG3 
Go to UniProtKB:  G1TPG3
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsLengthOrganismImage
18S ribosomal RNA21863Oryctolagus cuniculus
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsLengthOrganismImage
histone 4 (H4) mRNA336Mus musculus
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 39
MoleculeChainsLengthOrganismImage
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

View Full Validation Report



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