7TQL

CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining.

Lapointe, C.P.Grosely, R.Sokabe, M.Alvarado, C.Wang, J.Montabana, E.Villa, N.Shin, B.S.Dever, T.E.Fraser, C.S.Fernandez, I.S.Puglisi, J.D.

(2022) Nature 607: 185-190

  • DOI: https://doi.org/10.1038/s41586-022-04858-z
  • Primary Citation of Related Structures:  
    7TQL

  • PubMed Abstract: 

    Translation initiation defines the identity and quantity of a synthesized protein. The process is dysregulated in many human diseases 1,2 . A key commitment step is when the ribosomal subunits join at a translation start site on a messenger RNA to form a functional ribosome. Here, we combined single-molecule spectroscopy and structural methods using an in vitro reconstituted system to examine how the human ribosomal subunits join. Single-molecule fluorescence revealed when the universally conserved eukaryotic initiation factors eIF1A and eIF5B associate with and depart from initiation complexes. Guided by single-molecule dynamics, we visualized initiation complexes that contained both eIF1A and eIF5B using single-particle cryo-electron microscopy. The resulting structure revealed how eukaryote-specific contacts between the two proteins remodel the initiation complex to orient the initiator aminoacyl-tRNA in a conformation compatible with ribosomal subunit joining. Collectively, our findings provide a quantitative and architectural framework for the molecular choreography orchestrated by eIF1A and eIF5B during translation initiation in humans.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology College of Biological Sciences, University of California, Davis, CA, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5BA [auth 1]619Homo sapiensMutation(s): 4 
Gene Names: EIF5BIF2KIAA0741
EC: 3.6.5.3
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GTEx:  ENSG00000158417 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF1AD [auth 4]90Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173674 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS2E [auth B],
F [auth C]
419Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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GTEx:  ENSG00000168028 
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UniProt GroupsP61247P08865
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2G [auth D]218Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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GTEx:  ENSG00000140988 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformH [auth E]258Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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GTEx:  ENSG00000198034 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3I [auth F]225Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6J [auth G]226Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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GTEx:  ENSG00000137154 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7K [auth H]185Homo sapiensMutation(s): 0 
Gene Names: RPS7
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GTEx:  ENSG00000171863 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8L [auth I]205Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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GTEx:  ENSG00000142937 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9M [auth J]180Homo sapiensMutation(s): 0 
Gene Names: RPS9
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GTEx:  ENSG00000170889 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5N [auth K]189Homo sapiensMutation(s): 0 
Gene Names: RPS5
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GTEx:  ENSG00000083845 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11O [auth L]147Homo sapiensMutation(s): 0 
Gene Names: RPS11
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GTEx:  ENSG00000142534 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10P [auth M]97Homo sapiensMutation(s): 0 
Gene Names: RPS10
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GTEx:  ENSG00000124614 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS15Q [auth N]141Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS12R [auth O]120Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS11S [auth P]134Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15T [auth Q]115Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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GTEx:  ENSG00000115268 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16U [auth R]139Homo sapiensMutation(s): 0 
Gene Names: RPS16
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GTEx:  ENSG00000105193 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS17V [auth S]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS13W [auth T]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19X [auth U]139Homo sapiensMutation(s): 0 
Gene Names: RPS19
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GTEx:  ENSG00000105372 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS10Y [auth V]101Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aZ [auth W]129Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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GTEx:  ENSG00000134419 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23AA [auth X]141Homo sapiensMutation(s): 0 
Gene Names: RPS23
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GTEx:  ENSG00000186468 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 3 of 40S ribosomal protein S24BA [auth Y]123Homo sapiensMutation(s): 0 
Gene Names: RPS24
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GTEx:  ENSG00000138326 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21CA [auth Z]82Homo sapiensMutation(s): 0 
Gene Names: RPS21
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GTEx:  ENSG00000171858 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS25DA [auth a]72Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27EA [auth b]82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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GTEx:  ENSG00000177954 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26FA [auth c]99Homo sapiensMutation(s): 0 
Gene Names: RPS26
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GTEx:  ENSG00000197728 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS28GA [auth d]58Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS30HA [auth e]51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS14IA [auth f]54Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27aJA [auth g]65Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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GTEx:  ENSG00000143947 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eL41KA [auth h]19Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1LA [auth j]314Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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GTEx:  ENSG00000204628 
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S ribosomal RNAB [auth 2]1,656Homo sapiens
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Entity ID: 3
MoleculeChains LengthOrganismImage
Human Met-tRNAiMetC [auth 3]75Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Damon Runyon Cancer Research FoundationUnited StatesDRG-#2321-18
Knut and Alice Wallenberg FoundationSweden(KAW2015.0406
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States(GM011378

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2022-07-20
    Changes: Database references
  • Version 1.3: 2022-12-14
    Changes: Refinement description