5HYD

Crystal structure of calcium-free human S100Z


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Solving the crystal structure of human calcium-free S100Z: the siege and conquer of one of the last S100 family strongholds.

Calderone, V.Fragai, M.Gallo, G.Luchinat, C.

(2017) J Biol Inorg Chem 22: 519-526

  • DOI: 10.1007/s00775-017-1437-4
  • Primary Citation of Related Structures:  
    5HYD

  • PubMed Abstract: 
  • The X-ray structure of human apo-S100Z has been solved and compared with that of the zebrafish calcium-bound S100Z, which is the closest in sequence. Human apo-S100A12, which shows only 43% sequence identity to human S100Z, has been used as template ...

    The X-ray structure of human apo-S100Z has been solved and compared with that of the zebrafish calcium-bound S100Z, which is the closest in sequence. Human apo-S100A12, which shows only 43% sequence identity to human S100Z, has been used as template model to solve the crystallographic phase problem. Although a significant buried surface area between the two physiological dimers is present in the asymmetric unit of human apo-S100Z, the protein does not form the superhelical arrangement in the crystal as observed for the zebrafish calcium-bound S100Z and human calcium-bound S100A4. These findings further demonstrate that calcium plays a fundamental role in triggering quaternary structure formation in several S100s. Solving the X-ray structure of human apo-S100Z by standard molecular replacement procedures turned out to be a challenge and required trying different models and different software tools among which only one was successful. The model that allowed structure solution was that with one of the lowest sequence identity with the target protein among the S100 family in the apo state. Based on the previously solved zebrafish holo-S100Z, a putative human holo-S100Z structure has been then calculated through homology modeling; the differences between the experimental human apo and calculated holo structure have been compared to those existing for other members of the family.


    Related Citations: 
    • The crystal structure of zebrafish S100Z: implications for calcium-promoted S100 protein oligomerisation.
      Moroz, O.V., Bronstein, I.B., Wilson, K.S.
      (2011) J Mol Biol 411: 1072

    Organizational Affiliation

    Department of Chemistry Ugo Schiff, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein S100-ZABCD99Homo sapiensMutation(s): 0 
Gene Names: S100Z
Find proteins for Q8WXG8 (Homo sapiens)
Explore Q8WXG8 
Go to UniProtKB:  Q8WXG8
NIH Common Fund Data Resources
PHAROS  Q8WXG8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.326α = 90
b = 96.948β = 90
c = 115.572γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references