8A0E

CryoEM structure of DHS-eIF5A1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of human eIF5A-DHS complex reveals the molecular basis of hypusination-associated neurodegenerative disorders.

Wator, E.Wilk, P.Biela, A.Rawski, M.Zak, K.M.Steinchen, W.Bange, G.Glatt, S.Grudnik, P.

(2023) Nat Commun 14: 1698-1698

  • DOI: https://doi.org/10.1038/s41467-023-37305-2
  • Primary Citation of Related Structures:  
    7A6S, 7A6T, 8A0E, 8A0F, 8A0G

  • PubMed Abstract: 

    Hypusination is a unique post-translational modification of the eukaryotic translation factor 5A (eIF5A) that is essential for overcoming ribosome stalling at polyproline sequence stretches. The initial step of hypusination, the formation of deoxyhypusine, is catalyzed by deoxyhypusine synthase (DHS), however, the molecular details of the DHS-mediated reaction remained elusive. Recently, patient-derived variants of DHS and eIF5A have been linked to rare neurodevelopmental disorders. Here, we present the cryo-EM structure of the human eIF5A-DHS complex at 2.8 Å resolution and a crystal structure of DHS trapped in the key reaction transition state. Furthermore, we show that disease-associated DHS variants influence the complex formation and hypusination efficiency. Hence, our work dissects the molecular details of the deoxyhypusine synthesis reaction and reveals how clinically-relevant mutations affect this crucial cellular process.


  • Organizational Affiliation

    Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyhypusine synthase
A, B
371Homo sapiensMutation(s): 1 
Gene Names: DHPSDS
EC: 2.5.1.46
UniProt & NIH Common Fund Data Resources
Find proteins for P49366 (Homo sapiens)
Explore P49366 
Go to UniProtKB:  P49366
GTEx:  ENSG00000095059 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49366
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyhypusine synthase
C, D
371Homo sapiensMutation(s): 1 
Gene Names: DHPSDS
EC: 2.5.1.46
UniProt & NIH Common Fund Data Resources
Find proteins for P49366 (Homo sapiens)
Explore P49366 
Go to UniProtKB:  P49366
GTEx:  ENSG00000095059 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49366
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5A156Homo sapiensMutation(s): 0 
Gene Names: EIF5A
UniProt & NIH Common Fund Data Resources
Find proteins for P63241 (Homo sapiens)
Explore P63241 
Go to UniProtKB:  P63241
GTEx:  ENSG00000132507 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63241
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandUMO-2019/33/B/NZ1/01839
Foundation for Polish SciencePolandTEAM TECH CORE FACILITY/2017-4/6

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release