5HBF | pdb_00005hbf

Crystal structure of human full-length chitotriosidase (CHIT1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.245 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.205 (Depositor) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1) Reveals Features of Its Chitin Binding Domain.

Fadel, F.Zhao, Y.Cousido-Siah, A.Ruiz, F.X.Mitschler, A.Podjarny, A.

(2016) PLoS One 11: e0154190-e0154190

  • DOI: https://doi.org/10.1371/journal.pone.0154190
  • Primary Citation Related Structures: 
    5HBF

  • PubMed Abstract: 

    Chitinases are enzymes that catalyze the hydrolysis of chitin. Human chitotriosidase (CHIT1) is one of the two active human chitinases, involved in the innate immune response and highly expressed in a variety of diseases. CHIT1 is composed of a catalytic domain linked by a hinge to its chitin binding domain (ChBD). This latter domain belongs to the carbohydrate-binding module family 14 (CBM14 family) and facilitates binding to chitin. So far, the available crystal structures of the human chitinase CHIT1 and the Acidic Mammalian Chitinase (AMCase) comprise only their catalytic domain. Here, we report a crystallization strategy combining cross-seeding and micro-seeding cycles which allowed us to obtain the first crystal structure of the full length CHIT1 (CHIT1-FL) at 1.95 Å resolution. The CHIT1 chitin binding domain (ChBDCHIT1) structure shows a distorted β-sandwich 3D fold, typical of CBM14 family members. Accordingly, ChBDCHIT1 presents six conserved cysteine residues forming three disulfide bridges and several exposed aromatic residues that probably are involved in chitin binding, including the highly conserved Trp465 in a surface- exposed conformation. Furthermore, ChBDCHIT1 presents a positively charged surface which may be involved in electrostatic interactions. Our data highlight the strong structural conservation of CBM14 family members and uncover the structural similarity between the human ChBDCHIT1, tachycitin and house mite dust allergens. Overall, our new CHIT1-FL structure, determined with an adapted crystallization approach, is one of the few complete bi-modular chitinase structures available and reveals the structural features of a human CBM14 domain.


  • Organizational Affiliation
    • Department of Integrative Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch, France.

Macromolecule Content 

  • Total Structure Weight: 107.19 kDa 
  • Atom Count: 6,949 
  • Modeled Residue Count: 849 
  • Deposited Residue Count: 960 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chitotriosidase-1
A, B
480Homo sapiensMutation(s): 0 
Gene Names: CHIT1
EC: 3.2.1.14
UniProt & NIH Common Fund Data Resources
Find proteins for Q13231 (Homo sapiens)
Explore Q13231 
Go to UniProtKB:  Q13231
PHAROS:  Q13231
GTEx:  ENSG00000133063 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13231
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.245 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.205 (Depositor) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.143α = 90
b = 106.661β = 107.13
c = 85.67γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary