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: 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) ...

    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

    Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAA [auth a]216Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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GTEx:  ENSG00000168028 
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Entity ID: 2
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40S ribosomal protein S3aB [auth p]211Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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GTEx:  ENSG00000145425 
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Entity ID: 3
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40S ribosomal protein S2C [auth d]216Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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GTEx:  ENSG00000140988 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26D [auth Q]101Homo sapiensMutation(s): 0 
Gene Names: RPS26
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Entity ID: 5
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40S ribosomal protein S4, X isoformE [auth q]255Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 6
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60S ribosomal protein L41F [auth W]24Homo sapiensMutation(s): 0 
Gene Names: RPL41
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Entity ID: 7
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40S ribosomal protein S6G [auth r]222Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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Entity ID: 8
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40S ribosomal protein S7H [auth s]181Homo sapiensMutation(s): 0 
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40S ribosomal protein S8I [auth t]205Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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40S ribosomal protein S9J [auth c]180Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 11
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40S ribosomal protein S11K [auth n]144Homo sapiensMutation(s): 0 
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40S ribosomal protein S13L [auth m]149Homo sapiensMutation(s): 0 
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40S ribosomal protein S14M [auth i]125Homo sapiensMutation(s): 0 
Gene Names: RPS14
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40S ribosomal protein S21N [auth y]82Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 15
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40S ribosomal protein S15aO [auth f]129Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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GTEx:  ENSG00000134419 
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Entity ID: 16
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40S ribosomal protein S23P [auth j]139Homo sapiensMutation(s): 0 
Gene Names: RPS23
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40S ribosomal protein S24Q [auth z]122Homo sapiensMutation(s): 0 
Gene Names: RPS24
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40S ribosomal protein S27R82Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 19
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40S ribosomal protein S30S [auth T]44Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 21
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40S ribosomal protein S17U [auth w]130Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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40S ribosomal protein S16V [auth g]138Homo sapiensMutation(s): 0 
Gene Names: RPS16
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GTEx:  ENSG00000105193 
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Entity ID: 23
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40S ribosomal protein S3W [auth b]224Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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40S ribosomal protein S5X [auth e]189Homo sapiensMutation(s): 0 
Gene Names: RPS5
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40S ribosomal protein S10Y [auth u]95Homo sapiensMutation(s): 0 
Gene Names: RPS10
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40S ribosomal protein S12Z [auth v]116Homo sapiensMutation(s): 0 
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40S ribosomal protein S15AA [auth o]119Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 28
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40S ribosomal protein S18BA [auth k]140Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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GTEx:  ENSG00000231500 
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40S ribosomal protein S19CA [auth x]141Homo sapiensMutation(s): 0 
Gene Names: RPS19
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GTEx:  ENSG00000105372 
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40S ribosomal protein S20DA [auth h]98Homo sapiensMutation(s): 0 
Gene Names: RPS20
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40S ribosomal protein S25EA [auth P]70Homo sapiensMutation(s): 0 
Gene Names: RPS25
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40S ribosomal protein S28FA [auth S]61Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 33
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40S ribosomal protein S29GA [auth l]54Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 34
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Ubiquitin-40S ribosomal protein S27aHA [auth U]62Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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GTEx:  ENSG00000143947 
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Receptor of activated protein C kinase 1IA [auth V]309Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 36
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Eukaryotic translation initiation factor 3 subunit IJA [auth I]316Homo sapiensMutation(s): 0 
Gene Names: EIF3IEIF3S2TRIP1
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GTEx:  ENSG00000084623 
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Eukaryotic translation initiation factor 3 subunit BKA [auth B]566Homo sapiensMutation(s): 0 
Gene Names: EIF3BEIF3S9
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GTEx:  ENSG00000106263 
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Eukaryotic translation initiation factor 3 subunit ALA [auth A]722Homo sapiensMutation(s): 0 
Gene Names: EIF3AEIF3S10KIAA0139
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Eukaryotic translation initiation factor 3 subunit CMA [auth C]743Homo sapiensMutation(s): 0 
Gene Names: EIF3CEIF3S8
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit ENA [auth E]429Homo sapiensMutation(s): 0 
Gene Names: EIF3EEIF3S6INT6
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Find proteins for P60228 (Homo sapiens)
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PHAROS:  P60228
GTEx:  ENSG00000104408 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit FOA [auth F]269Homo sapiensMutation(s): 0 
Gene Names: EIF3FEIF3S5
EC: 3.4.19.12
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Find proteins for O00303 (Homo sapiens)
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PHAROS:  O00303
GTEx:  ENSG00000175390 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit HPA [auth H]318Homo sapiensMutation(s): 0 
Gene Names: EIF3HEIF3S3
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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
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit KQA [auth K]217Homo sapiensMutation(s): 0 
Gene Names: EIF3KEIF3S12ARG134HSPC029MSTP001PTD001
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GTEx:  ENSG00000178982 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit LRA [auth L]372Homo sapiensMutation(s): 0 
Gene Names: EIF3LEIF3EIPEIF3S6IPHSPC021HSPC025MSTP005
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GTEx:  ENSG00000100129 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit MSA [auth M]362Homo sapiensMutation(s): 0 
Gene Names: EIF3MHFLB5PCID1GA17PNAS-125
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PHAROS:  Q7L2H7
GTEx:  ENSG00000149100 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-binding cassette sub-family E member 1TA [auth 1]595Homo sapiensMutation(s): 0 
Gene Names: ABCE1RLIRNASEL1RNASELIRNS4IOK/SW-cl.40
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Find proteins for P61221 (Homo sapiens)
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GTEx:  ENSG00000164163 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1UA [auth N]91Homo sapiensMutation(s): 0 
Gene Names: EIF1SUI1
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Find proteins for P41567 (Homo sapiens)
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GTEx:  ENSG00000173812 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit DVA [auth D]527Homo sapiensMutation(s): 0 
Gene Names: EIF3DEIF3S7
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GTEx:  ENSG00000100353 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
RNA recognition motif (unknown)WA [auth Y]78Homo sapiensMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit JXA [auth G],
YA [auth J]
258Homo sapiensMutation(s): 0 
Gene Names: EIF3JEIF3S1PRO0391
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GTEx:  ENSG00000104131 
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Entity ID: 20
MoleculeChainsLengthOrganismImage
18S ribosomal RNAT [auth 2]1720Homo sapiens
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Small Molecules
Ligands 5 Unique
IDChainsName / 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
 Ligand Interaction
ADP
Query on ADP

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

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CB [auth 1],
DB [auth 1]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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

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

Experimental Data

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

Structure Validation

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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