7C3D

Crystal structure of AofleA from Arthrobotrys oligospora in complex with D-arabinose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural insights into the fungi-nematodes interaction mediated by fucose-specific lectin AofleA from Arthrobotrys oligospora.

Liu, M.Cheng, X.Wang, J.Tian, D.Tang, K.Xu, T.Zhang, M.Wang, Y.Wang, M.

(2020) Int J Biol Macromol 164: 783-793

  • DOI: https://doi.org/10.1016/j.ijbiomac.2020.07.173
  • Primary Citation of Related Structures:  
    7C37, 7C38, 7C39, 7C3C, 7C3D, 7C3E

  • PubMed Abstract: 

    Fungal lectin can bind specific carbohydrate structures of the host and work in recognition and adhesion or as a toxic factor. AofleA, as a fucose-specific lectin from widely studied nematode predatory fungus Arthrobotrys oligospora, possibly plays a key role in the event of capturing nematodes, but the mechanism remains unknown. Here we report the crystal structure of AofleA, which exists as a homodimer with each subunit folds as a six-bladed β-propeller. Our structural and biological results revealed that three of the six putative binding sites of AofleA had fucose-binding abilities. In addition, we found that AofleA could bind to the pharynx and intestine of the nematode in a fucose-binding-dependent manner. Our results facilitate the understanding of the mechanism that fucose-specific lectin mediates fungi-nematodes interaction, and provide structural information for the development of potential applications of AofleA.


  • Organizational Affiliation

    School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AofleA
A, B
355Orbilia oligospora ATCC 24927Mutation(s): 0 
Gene Names: AOL_s00076g540
UniProt
Find proteins for G1XA82 (Arthrobotrys oligospora (strain ATCC 24927 / CBS 115.81 / DSM 1491))
Explore G1XA82 
Go to UniProtKB:  G1XA82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1XA82
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
64K (Subject of Investigation/LOI)
Query on 64K

Download Ideal Coordinates CCD File 
D [auth A]alpha-D-arabinopyranose
C5 H10 O5
SRBFZHDQGSBBOR-MBMOQRBOSA-N
SEJ (Subject of Investigation/LOI)
Query on SEJ

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
beta-D-arabinopyranose
C5 H10 O5
SRBFZHDQGSBBOR-SQOUGZDYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.707α = 90
b = 79.054β = 90
c = 135.066γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770066
Other governmentChinaKJ2019ZD02

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2020-08-12
    Changes: Database references, Structure summary
  • Version 1.3: 2020-09-23
    Changes: Structure summary
  • Version 1.4: 2023-11-29
    Changes: Data collection, Database references, Refinement description