6Z1N

Structure of the human heterotetrameric cis-prenyltransferase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex.

Bar-El, M.L.Vankova, P.Yeheskel, A.Simhaev, L.Engel, H.Man, P.Haitin, Y.Giladi, M.

(2020) Nat Commun 11: 5273-5273

  • DOI: https://doi.org/10.1038/s41467-020-18970-z
  • Primary Citation of Related Structures:  
    6Z1N

  • PubMed Abstract: 

    The human cis-prenyltransferase (hcis-PT) is an enzymatic complex essential for protein N-glycosylation. Synthesizing the precursor of the glycosyl carrier dolichol-phosphate, mutations in hcis-PT cause severe human diseases. Here, we reveal that hcis-PT exhibits a heterotetrameric assembly in solution, consisting of two catalytic dehydrodolichyl diphosphate synthase (DHDDS) and inactive Nogo-B receptor (NgBR) heterodimers. Importantly, the 2.3 Å crystal structure reveals that the tetramer assembles via the DHDDS C-termini as a dimer-of-heterodimers. Moreover, the distal C-terminus of NgBR transverses across the interface with DHDDS, directly participating in active-site formation and the functional coupling between the subunits. Finally, we explored the functional consequences of disease mutations clustered around the active-site, and in combination with molecular dynamics simulations, we propose a mechanism for hcis-PT dysfunction in retinitis pigmentosa. Together, our structure of the hcis-PT complex unveils the dolichol synthesis mechanism and its perturbation in disease.


  • Organizational Affiliation

    Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 6997801, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dehydrodolichyl diphosphate synthase complex subunit DHDDS340Homo sapiensMutation(s): 0 
Gene Names: DHDDSHDS
EC: 2.5.1.87
UniProt & NIH Common Fund Data Resources
Find proteins for Q86SQ9 (Homo sapiens)
Explore Q86SQ9 
Go to UniProtKB:  Q86SQ9
PHAROS:  Q86SQ9
GTEx:  ENSG00000117682 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86SQ9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dehydrodolichyl diphosphate synthase complex subunit NUS1219Homo sapiensMutation(s): 0 
Gene Names: NUS1C6orf68NGBR
EC: 2.5.1.87
UniProt & NIH Common Fund Data Resources
Find proteins for Q96E22 (Homo sapiens)
Explore Q96E22 
Go to UniProtKB:  Q96E22
PHAROS:  Q96E22
GTEx:  ENSG00000153989 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96E22
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.074α = 90
b = 184.074β = 90
c = 112.593γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MrBUMPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael1721/16
Israel Science FoundationIsrael1775/12
Other privateIsraelICRF-01214
Other privateIsraelICRF-19202
German-Israeli Foundation for Research and DevelopmentIsraelI2425418.13-2016

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description