7WDL

Fungal immunomodulatory protein FIP-nha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Linking the thermostability of FIP-nha (Nectria haematococca) to its structural properties.

Liu, Y.Bastiaan-Net, S.Zhang, Y.Hoppenbrouwers, T.Xie, Y.Wang, Y.Wei, X.Du, G.Zhang, H.Imam, K.M.D.S.U.Wichers, H.Li, Z.

(2022) Int J Biol Macromol 213: 555-564

  • DOI: https://doi.org/10.1016/j.ijbiomac.2022.05.136
  • Primary Citation of Related Structures:  
    7WDL

  • PubMed Abstract: 

    Fungal immunomodulatory proteins (FIPs) have been investigated for their use as potential natural derived anti-tumor molecules. However, the stability of FIPs is critical for their preparation and storage. In this study, the correlation between thermal stability and protein structural features of rFIP-nha, with significant anti-tumor activity, has been evaluated. For comprehensive analysis, FIP-nha and its homologues FIP-gmi, FIP-fve, and LZ-8 were all recombinantly expressed in E. coli. In solution, rFIP-nha and rFIP-gmi formed tetramers; rFIP-fve and rLZ-8 appeared as dimers. Their melting temperatures were 85.1 °C, 77.8 °C, 66.5 °C, and 64.4 °C, respectively. Accordingly, their cytotoxicity was also temperature dependent. To investigate the underlying mechanism of their thermostability, we solved the crystal structure of FIP-nha. Detailed structure analysis, molecular dynamic simulation and mutagenesis studies indicated that a higher thermostability was correlated to higher oligomerization states, larger interface area, and more interactions. The structure property studies indicate that Y12, D61 and Y108 were critical for oligomerization and high thermostability of rFIP-nha, but the dimeric and tetrameric states of rFIP-nha exert similar cytotoxicity on A549 cells. Taken together, these findings reveal that thermostability of FIPs was dependent on their oligomerization state, and correlated with their cytotoxicity.


  • Organizational Affiliation

    Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agriculture Sciences, Beijing 100193, China; Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen 6708WG, the Netherlands; Laboratory of Food Chemistry, Wageningen University, Wageningen 6708WG, the Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fungal immunomodulatory proteinA [auth B],
B [auth A],
C,
D
122Fusarium solaniMutation(s): 0 
Gene Names: NECHADRAFT_88285
UniProt
Find proteins for C7ZE17 (Fusarium vanettenii (strain ATCC MYA-4622 / CBS 123669 / FGSC 9596 / NRRL 45880 / 77-13-4))
Explore C7ZE17 
Go to UniProtKB:  C7ZE17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7ZE17
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.256α = 90
b = 119.453β = 90
c = 110.224γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina2017YFD0400204
Other governmentNetherlandsKB-37-001-007

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description