6FEC

Human cap-dependent 48S pre-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a human cap-dependent 48S translation pre-initiation complex.

Eliseev, B.Yeramala, L.Leitner, A.Karuppasamy, M.Raimondeau, E.Huard, K.Alkalaeva, E.Aebersold, R.Schaffitzel, C.

(2018) Nucleic Acids Res 46: 2678-2689

  • DOI: https://doi.org/10.1093/nar/gky054
  • Primary Citation of Related Structures:  
    6FEC

  • PubMed Abstract: 

    Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load the mRNA onto the 43S pre-initiation complex comprising 40S and initiation factors 1, 1A, 2, 3 and 5 as well as initiator-tRNA. Binding of the mRNA is followed by mRNA scanning in the 48S pre-initiation complex, until a start codon is recognised. Here, we use a reconstituted system to prepare human 48S complexes assembled on capped mRNA in the presence of eIF4B and eIF4F. The highly purified h-48S complexes are used for cross-linking/mass spectrometry, revealing the protein interaction network in this complex. We report the electron cryo-microscopy structure of the h-48S complex at 6.3 Å resolution. While the majority of eIF4B and eIF4F appear to be flexible with respect to the ribosome, additional density is detected at the entrance of the 40S mRNA channel which we attribute to the RNA-recognition motif of eIF4B. The eight core subunits of eIF3 are bound at the 40S solvent-exposed side, as well as the subunits eIF3d, eIF3b and eIF3i. elF2 and initiator-tRNA bound to the start codon are present at the 40S intersubunit side. This cryo-EM structure represents a molecular snap-shot revealing the h-48S complex following start codon recognition.


  • Organizational Affiliation

    School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit AA [auth 1]1,362Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit CB [auth 2]843Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit EC [auth 3]445Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104408 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit FD [auth 4]364Homo sapiensMutation(s): 0 
EC: 3.4.19.12
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit HE [auth 5]352Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit KF [auth 6]218Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000178982 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit LG [auth 7]564Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100129 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit MH [auth 8]374Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149100 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT DI [auth 9]368Homo sapiensMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11L [auth G]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16M [auth H]141Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformN [auth I]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29O [auth J]53Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9P [auth K]182Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18Q [auth L]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1S [auth P]266Homo sapiensMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23T [auth Q]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19U [auth R]141Homo sapiensMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 3V [auth S]422Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130741 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5W [auth U]191Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30X [auth V]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25Y [auth W]75Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7Z [auth X]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27AA [auth Y]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13BA [auth Z]150Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aCA [auth a]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21DA [auth b]82Homo sapiensMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2EA [auth c]226Homo sapiensMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT (eIF2-Beta)FA [auth d]17Homo sapiensMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17GA [auth e]126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAHA [auth f]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3IA [auth g]227Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20JA [auth h]104Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aKA [auth i]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14LA [auth j]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26MA [auth k]99Homo sapiensMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28NA [auth l]64Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1OA [auth m]313Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15PA [auth n]127Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8QA [auth o]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aRA [auth p]71Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6SA [auth q]237Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12TA [auth r]124Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24UA [auth s]131Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10VA [auth t]98Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4BWA [auth u]636Homo sapiensMutation(s): 0 
Gene Names: EIF4B
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GTEx:  ENSG00000063046 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit BXA [auth w]1,121Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains LengthOrganismImage
18S ribosomal RNAJ [auth A]1,776Homo sapiens
Sequence Annotations
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  • Reference Sequence
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Entity ID: 11
MoleculeChains LengthOrganismImage
Messenger RNA (26-MER)K [auth F]26Homo sapiens
Sequence Annotations
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  • Reference Sequence
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Entity ID: 18
MoleculeChains LengthOrganismImage
Transfer RNA (75-MER)R [auth N]75Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0194
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilBelgium281331
EMBL-RFBRBelgium15-54-74001

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Refinement description