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 

wwPDB Validation 3D Report Full Report



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: 10.1038/s41467-020-14603-7
  • Structures With Same Primary Citation

  • 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 p ...

    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. irmi.sinning@bzh.uni-heidelberg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferation-associated protein 2G4A394Homo sapiensMutation(s): 0 
Gene Names: PA2G4EBP1
Find proteins for Q9UQ80 (Homo sapiens)
Explore Q9UQ80 
Go to UniProtKB:  Q9UQ80
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PHAROS  Q9UQ80
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35Lh123Homo sapiensMutation(s): 0 
Gene Names: RPL35
Find proteins for P42766 (Homo sapiens)
Explore P42766 
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PHAROS  P42766
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38Lk70Homo sapiensMutation(s): 0 
Gene Names: RPL38
Find proteins for P63173 (Homo sapiens)
Explore P63173 
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PHAROS  P63173
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19LR196Homo sapiensMutation(s): 0 
Gene Names: RPL19
Find proteins for P84098 (Homo sapiens)
Explore P84098 
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PHAROS  P84098
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23aLX156Homo sapiensMutation(s): 0 
Gene Names: RPL23A
Find proteins for P62750 (Homo sapiens)
Explore P62750 
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PHAROS  P62750
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26LY145Homo sapiensMutation(s): 0 
Gene Names: RPL26
Find proteins for P61254 (Homo sapiens)
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PHAROS  P61254
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  • Reference Sequence

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Entity ID: 7
MoleculeChainsLengthOrganism
28S ribosomal RNA including ES27L-B (2839-3265)L55070Homo sapiens

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Entity ID: 8
MoleculeChainsLengthOrganism
5.8S ribosomal RNAL8157Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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)GermanyLeibniz SI 586/6-1

Revision History 

  • Version 1.0: 2020-02-19
    Type: Initial release