7O88

Cystal structure of Zymogen Granule Protein 16 (ZG16)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conformational switches and redox properties of the colon cancer-associated human lectin ZG16.

Javitt, G.Kinzel, A.Reznik, N.Fass, D.

(2021) FEBS J 288: 6465-6475

  • DOI: https://doi.org/10.1111/febs.16044
  • Primary Citation of Related Structures:  
    7O3I, 7O4P, 7O88

  • PubMed Abstract: 

    Zymogen granule membrane protein 16 (ZG16) is produced in organs that secrete large quantities of enzymes and other proteins into the digestive tract. ZG16 binds microbial pathogens, and lower ZG16 expression levels correlate with colorectal cancer, but the physiological function of the protein is poorly understood. One prominent attribute of ZG16 is its ability to bind glycans, but other aspects of the protein may also contribute to activity. An intriguing feature of ZG16 is a CXXC motif at the carboxy terminus. Here, we describe crystal structures and biochemical studies showing that the CXXC motif is on a flexible tail, where it contributes little to structure or stability but is available to engage in redox reactions. Specifically, we demonstrate that the ZG16 cysteine thiols can be oxidized to a disulfide by quiescin sulfhydryl oxidase 1, which is a sulfhydryl oxidase present together with ZG16 in the Golgi apparatus and in mucus, as well as by protein disulfide isomerase. ZG16 crystal structures also draw attention to a nonproline cis peptide bond that can isomerize within the protein and to the mobility of glycine-rich loops in the glycan-binding site. An understanding of the properties of the ZG16 CXXC motif and the discovery of internal conformational switches extend existing knowledge relating to the glycan-binding activity of the protein.


  • Organizational Affiliation

    Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zymogen granule membrane protein 16
A, B
148Homo sapiensMutation(s): 3 
Gene Names: ZG16
UniProt & NIH Common Fund Data Resources
Find proteins for O60844 (Homo sapiens)
Explore O60844 
Go to UniProtKB:  O60844
PHAROS:  O60844
GTEx:  ENSG00000174992 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60844
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.978α = 90
b = 45.418β = 90
c = 146.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description