6ZVJ

Structure of a human ABCE1-bound 43S pre-initiation complex - State II


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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

A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes.

Kratzat, H.Mackens-Kiani, T.Ameismeier, M.Potocnjak, M.Cheng, J.Dacheux, E.Namane, A.Berninghausen, O.Herzog, F.Fromont-Racine, M.Becker, T.Beckmann, R.

(2021) EMBO J 40: e105179-e105179

  • DOI: https://doi.org/10.15252/embj.2020105179
  • Primary Citation of Related Structures:  
    6ZCE, 6ZU9, 6ZVJ, 7A09, 7A1G

  • PubMed Abstract: 

    In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. These comprise/include the large eIF3 complex, eIF3j (Hcr1 in yeast) and the ATP-binding cassette protein ABCE1 (Rli1 in yeast). The ATPase is mainly active as a recycling factor, but it can remain bound to the dissociated 40S subunit until formation of the next 43S pre-initiation complexes. However, its functional role and native architectural context remains largely enigmatic. Here, we present an architectural inventory of native yeast and human ABCE1-containing pre-initiation complexes by cryo-EM. We found that ABCE1 was mostly associated with early 43S, but also with later 48S phases of initiation. It adopted a novel hybrid conformation of its nucleotide-binding domains, while interacting with the N-terminus of eIF3j. Further, eIF3j occupied the mRNA entry channel via its ultimate C-terminus providing a structural explanation for its antagonistic role with respect to mRNA binding. Overall, the native human samples provide a near-complete molecular picture of the architecture and sophisticated interaction network of the 43S-bound eIF3 complex and the eIF2 ternary complex containing the initiator tRNA.


  • Organizational Affiliation

    Génétique des Interactions Macromoléculaires, UMR3525 CNRS, Institut Pasteur, Paris, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAA [auth a]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aB [auth p]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2C [auth d]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26D [auth Q]101Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE [auth q]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41F [auth W]24Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6G [auth r]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7H [auth s]181Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8I [auth t]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9J [auth c]180Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11K [auth n]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13L [auth m]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14M [auth i]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21N [auth y]82Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aO [auth f]129Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23P [auth j]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24Q [auth z]122Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2782Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30S [auth T]44Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17U [auth w]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16V [auth g]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3W [auth b]224Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5X [auth e]189Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10Y [auth u]95Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12Z [auth v]116Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15AA [auth o]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18BA [auth k]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19CA [auth x]141Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20DA [auth h]98Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25EA [auth P]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28FA [auth S]61Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29GA [auth l]54Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aHA [auth U]62Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1IA [auth V]309Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit IJA [auth I]316Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000084623 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit BKA [auth B]566Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106263 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit ALA [auth A]722Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000107581 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit CMA [auth C]743Homo sapiensMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit ENA [auth E]429Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104408 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit FOA [auth F]269Homo sapiensMutation(s): 0 
EC: 3.4.19.12
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GTEx:  ENSG00000175390 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit HPA [auth H]318Homo sapiensMutation(s): 0 
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Find proteins for O15372 (Homo sapiens)
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PHAROS:  O15372
GTEx:  ENSG00000147677 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit KQA [auth K]217Homo sapiensMutation(s): 0 
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PHAROS:  Q9UBQ5
GTEx:  ENSG00000178982 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit LRA [auth L]372Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100129 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit MSA [auth M]362Homo sapiensMutation(s): 0 
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PHAROS:  Q7L2H7
GTEx:  ENSG00000149100 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-binding cassette sub-family E member 1TA [auth 1]595Homo sapiensMutation(s): 0 
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Find proteins for P61221 (Homo sapiens)
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GTEx:  ENSG00000164163 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1UA [auth N]91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173812 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit DVA [auth D]527Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100353 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
RNA recognition motif (unknown)WA [auth Y]78Homo sapiensMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit JXA [auth G],
YA [auth J]
258Homo sapiensMutation(s): 0 
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Find proteins for O75822 (Homo sapiens)
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GTEx:  ENSG00000104131 
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Entity ID: 20
MoleculeChains LengthOrganismImage
18S ribosomal RNAT [auth 2]1,720Homo sapiens
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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GB [auth 1]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

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EB [auth 1]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4
Query on SF4

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CB [auth 1],
DB [auth 1]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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AB [auth l],
BB [auth U],
ZA [auth Q]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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FB [auth 1],
HB [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2021-01-13
    Changes: Database references