6YAM

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS3F227Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
eukaryotic translation initiation factor 1Aj144Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eS7J190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS8K206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS4L182Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS10M98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS17N158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS12O132Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uS15P150Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS11Q151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS9S141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS17T135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
60s ribosomal protein l41l25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS19V145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS10W119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS21X82Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS8Y130Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS12Z142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS24a133Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TS40 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS26b115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS27c84Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS28d69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uS14e53Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS2C208Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSA
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eS31f71Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein RACK1g313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eS25n75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS30i59Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
eukaryotic translation initiation factor 2 subunit alphaA266Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF2S1
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
eukaryotic translation initiation factor 2 subunit gammaB422Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-binding cassette sub-family E member 1 (ABCE1)k595Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS13U152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS1D264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS19R145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
eukaryotic translation initiation factor 3 subunit dm548Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit Ay1350Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3AEIF3S10
Find proteins for A0A5F9C991 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit Cv913Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3CEIF3S8
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit Ew445Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3EEIF3S6INT6
Find proteins for G1SUC8 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit Fq272Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3FEIF3S5
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
eukaryotic translation initiation factor 3 subunit hr352Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit Ks218Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3KEIF3S12
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
eukaryotic translation initiation factor 3 subunit lt564Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS5E226Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit Mu374Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3M
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS4G263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS7H191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for U3KMN4 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS6I237Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 1
MoleculeChainsLengthOrganismImage
initiator methionylated tRNA175Oryctolagus cuniculus
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Entity ID: 34
MoleculeChainsLengthOrganismImage
18S ribosomal RNA21863Oryctolagus cuniculus
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Entity ID: 41
MoleculeChainsLengthOrganismImage
beta-globin mRNA345Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

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k
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
SF4
Query on SF4

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k
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MG
Query on MG

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k
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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