Crystal structure analysis of msp domain

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.213 

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Elimination of the native structure and solubility of the hVAPB MSP domain by the Pro56Ser mutation that causes amyotrophic lateral sclerosis.

Shi, J.Lua, S.Tong, J.S.Song, J.

(2010) Biochemistry 49: 3887-3897

  • DOI: https://doi.org/10.1021/bi902057a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Pro56Ser mutation in the human VAPB MSP domain causes a familial amyotrophic lateral sclerosis. Here we present the first structural investigation of both wild-type and Pro56Ser mutant MSP domains. The results reveal that the wild-type MSP domain is well-folded at neutral pH but can undergo acid-induced unfolding reversibly. It has a thermodynamic stability energy (DeltaG degrees (N-U)) of 7.40 kcal/mol and is also active in binding to a Nir2 peptide with a K(D) of 0.65 muM. Further determination of its crystal structure reveals that it adopts a seven-strand immunoglobulin-like beta sandwich in which Pro56 adopts the unusual cis-peptide bond conformation that appears to be critical in maintaining the characteristic S-shaped loop. Markedly, the Pro56Ser mutation renders the MSP domain insoluble in buffer. Nevertheless, as facilitated by our recent discovery that "insoluble proteins" can be solubilized in salt-free water, we have successfully characterized the residue-specific conformation of the Pro56Ser mutant by CD and heteronuclear NMR spectroscopy. The Pro56Ser mutant remains lacking of the native tight packing and secondary structures under various conditions and was further characterized as having a non-native helical conformation weakly populated at pH 3.5. Intriguingly, Pro12 located in another S-shaped loop also adopts the cis-peptide bond conformation, and its mutation to Ser is able to make the MSP domain highly insoluble and unfolded like the Pro56Ser mutant. Our study thus implies that the Pro56Ser mutation might lead to ALS by eliminating the native MSP structure, which consequently leads to aggregation and loss of functions under physiological conditions.

  • Organizational Affiliation

    Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vesicle-associated membrane protein-associated protein B/C
A, B
127Homo sapiensMutation(s): 0 
Gene Names: UNQ484/PRO983VAPB
UniProt & NIH Common Fund Data Resources
Find proteins for O95292 (Homo sapiens)
Explore O95292 
Go to UniProtKB:  O95292
PHAROS:  O95292
GTEx:  ENSG00000124164 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95292
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.213 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.024α = 90
b = 144.024β = 90
c = 34.791γ = 120
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description