8WB2

Heme-bound Arabidopsis thaliana temperature-induced lipocalin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystallographic and functional studies of a plant temperature-induced lipocalin.

Dong, C.S.Zhang, W.L.Wang, X.Y.Wang, X.Wang, J.Wang, M.Fang, Y.Liu, L.

(2023) Biochim Biophys Acta Gen Subj 1868: 130540-130540

  • DOI: https://doi.org/10.1016/j.bbagen.2023.130540
  • Primary Citation of Related Structures:  
    8WB2

  • PubMed Abstract: 

    Arabidopsis thaliana temperature-induced lipocalin (AtTIL) is a prototypical member of plant lipocalins and participates in a variety of cellular processes, particularly stress responses. Bioinformatical and physiological studies have proposed its promiscuous ligand-binding ability, but the molecular basis is yet unclear. Here, we report the 1.9-Å crystal structure of AtTIL in complex with heme. Spectrophotometric absorbance titration with heme yields a dissociation constant of ∼2 micromolar, indicating the relatively weak interaction between AtTIL and heme, which is confirmed by the AtTIL-heme structure. Although binding to retinal or biliverdin is not detected, such possibility can not be precluded as suggested by comparison with other lipocalin structures. These results show that AtTIL is a structural and functional homolog of the bacterial lipocalin Blc.


  • Organizational Affiliation

    School of Life Sciences, Anhui University, Hefei, Anhui 230601, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Temperature-induced lipocalin-1206Arabidopsis thalianaMutation(s): 0 
Gene Names: TILAt5g58070K21L19.6
UniProt
Find proteins for Q9FGT8 (Arabidopsis thaliana)
Explore Q9FGT8 
Go to UniProtKB:  Q9FGT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FGT8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.685α = 90
b = 75.685β = 90
c = 208.238γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
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)China32000444
National Natural Science Foundation of China (NSFC)China32201041

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-01-03
    Changes: Database references