5H0Q

Crystal structure of lipid binding protein Nakanori at 1.5A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A novel sphingomyelin/cholesterol domain-specific probe reveals the dynamics of the membrane domains during virus release and in Niemann-Pick type C

Makino, A.Abe, M.Ishitsuka, R.Murate, M.Kishimoto, T.Sakai, S.Hullin-Matsuda, F.Shimada, Y.Inaba, T.Miyatake, H.Tanaka, H.Kurahashi, A.Pack, C.G.Kasai, R.S.Kubo, S.Schieber, N.L.Dohmae, N.Tochio, N.Hagiwara, K.Sasaki, Y.Aida, Y.Fujimori, F.Kigawa, T.Nishibori, K.Parton, R.G.Kusumi, A.Sako, Y.Anderluh, G.Yamashita, M.Kobayashi, T.Greimel, P.Kobayashi, T.

(2017) FASEB J 31: 1301-1322

  • DOI: https://doi.org/10.1096/fj.201500075R
  • Primary Citation of Related Structures:  
    5H0Q

  • PubMed Abstract: 

    We identified a novel, nontoxic mushroom protein that specifically binds to a complex of sphingomyelin (SM), a major sphingolipid in mammalian cells, and cholesterol (Chol). The purified protein, termed nakanori, labeled cell surface domains in an SM- and Chol-dependent manner and decorated specific lipid domains that colocalized with inner leaflet small GTPase H-Ras, but not K-Ras. The use of nakanori as a lipid-domain-specific probe revealed altered distribution and dynamics of SM/Chol on the cell surface of Niemann-Pick type C fibroblasts, possibly explaining some of the disease phenotype. In addition, that nakanori treatment of epithelial cells after influenza virus infection potently inhibited virus release demonstrates the therapeutic value of targeting specific lipid domains for anti-viral treatment.-Makino, A., Abe, M., Ishitsuka, R., Murate, M., Kishimoto, T., Sakai, S., Hullin-Matsuda, F., Shimada, Y., Inaba, T., Miyatake, H., Tanaka, H., Kurahashi, A., Pack, C.-G., Kasai, R. S., Kubo, S., Schieber, N. L., Dohmae, N., Tochio, N., Hagiwara, K., Sasaki, Y., Aida, Y., Fujimori, F., Kigawa, T., Nishibori, K., Parton, R. G., Kusumi, A., Sako, Y., Anderluh, G., Yamashita, M., Kobayashi, T., Greimel, P., Kobayashi, T. A novel sphingomyelin/cholesterol domain-specific probe reveals the dynamics of the membrane domains during virus release and in Niemann-Pick type C.


  • Organizational Affiliation

    Rikagaku Kenkyūsho (RIKEN), Saitama, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipid binding protein202Grifola frondosaMutation(s): 0 
UniProt
Find proteins for A0A1D5B380 (Grifola frondosa)
Explore A0A1D5B380 
Go to UniProtKB:  A0A1D5B380
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D5B380
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.763α = 90
b = 75.763β = 90
c = 92.804γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Structure summary
  • Version 1.2: 2017-04-12
    Changes: Database references
  • Version 1.3: 2017-08-16
    Changes: Data collection, Structure summary
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references
  • Version 1.5: 2024-04-03
    Changes: Refinement description