6YAL

Mammalian 48S late-stage initiation complex with beta-globin mRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS7J192Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SVB0 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS8K206Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100352057
Find proteins for G1TJW1 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS4L182Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS10M98Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348511
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS17N158Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS12O132Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS15P150Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS11Q151Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS14
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS9S141Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS16
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS17T135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353606RPS17
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
60s ribosomal protein ul41l25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS19V141Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345774
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS10W119Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS20LOC100341365LOC100348955LOC100354063
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS21X82Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS21
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS8Y130Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS12Z143Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS23
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS24a133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS26b115Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100346996
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS27c84Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345694LOC100345044LOC100348261RPS27
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS28d69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS14e56Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS2C209Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSALOC100144340
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS31f71Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein RACK1g313Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS25n124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS30i133Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 2 subunit alphaA284Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF2S1
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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: 37
MoleculeChainsSequence LengthOrganismDetails
eukaryotic translation initiation factor 1Aj111Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100339548
Find proteins for G1SYS4 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ATP-binding cassette sub-family E member 1 (ABCE1)k595Oryctolagus cuniculusMutation(s): 0 
Gene Names: ABCE1
Find proteins for G1SG72 (Oryctolagus cuniculus)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS13U152Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS1D264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
Find proteins for G1TN72 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS19R145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein uS5E226Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein uS3F243Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS4G263Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100338112
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein uS7H191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein eS6I237Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS6
Find proteins for A0A5K1UJS7 (Oryctolagus cuniculus)
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Entity ID: 1
MoleculeChainsLengthOrganism
initiator methionylated tRNA175Oryctolagus cuniculus

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Entity ID: 34
MoleculeChainsLengthOrganism
18S ribosomal RNA21863Oryctolagus cuniculus

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Entity ID: 41
MoleculeChainsLengthOrganism
beta-globin mRNA342Homo 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: 3.00 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