6SXO

Cryo-EM structure of the human Ebp1-ribosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments.

Wild, K.Aleksic, M.Lapouge, K.Juaire, K.D.Flemming, D.Pfeffer, S.Sinning, I.

(2020) Nat Commun 11: 776-776

  • DOI: https://doi.org/10.1038/s41467-020-14603-7
  • Primary Citation of Related Structures:  
    6SXO

  • PubMed Abstract: 

    Human Ebp1 is a member of the proliferation-associated 2G4 (PA2G4) family and plays an important role in cancer regulation. Ebp1 shares the methionine aminopeptidase (MetAP) fold and binds to mature 80S ribosomes for translational control. Here, we present a cryo-EM single particle analysis reconstruction of Ebp1 bound to non-translating human 80S ribosomes at a resolution range from 3.3 to ~8 Å. Ebp1 blocks the tunnel exit with major interactions to the general uL23/uL29 docking site for nascent chain-associated factors complemented by eukaryote-specific eL19 and rRNA helix H59. H59 is defined as dynamic adaptor undergoing significant remodeling upon Ebp1 binding. Ebp1 recruits rRNA expansion segment ES27L to the tunnel exit via specific interactions with rRNA consensus sequences. The Ebp1-ribosome complex serves as a template for MetAP binding and provides insights into the structural principles for spatial coordination of co-translational events and molecular triage at the ribosomal tunnel exit.


  • Organizational Affiliation

    Biochemiezentrum der Universität Heidelberg (BZH), INF 328, D-69120, Heidelberg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferation-associated protein 2G4394Homo sapiensMutation(s): 0 
Gene Names: PA2G4EBP1
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PHAROS:  Q9UQ80
GTEx:  ENSG00000170515 
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UniProt GroupQ9UQ80
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35B [auth Lh]123Homo sapiensMutation(s): 0 
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Find proteins for P42766 (Homo sapiens)
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PHAROS:  P42766
GTEx:  ENSG00000136942 
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UniProt GroupP42766
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38C [auth Lk]70Homo sapiensMutation(s): 0 
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Find proteins for P63173 (Homo sapiens)
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GTEx:  ENSG00000172809 
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UniProt GroupP63173
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19D [auth LR]196Homo sapiensMutation(s): 0 
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Find proteins for P84098 (Homo sapiens)
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GTEx:  ENSG00000108298 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aE [auth LX]156Homo sapiensMutation(s): 0 
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PHAROS:  P62750
GTEx:  ENSG00000198242 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26F [auth LY]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 7
MoleculeChains LengthOrganismImage
28S ribosomal RNA including ES27L-B (2839-3265)G [auth L5]5,070Homo sapiens
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Entity ID: 8
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAH [auth L8]157Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyLeibniz SI 586/6-1

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection, Database references