6DS2

Crystal structure of Ni(II)-bound human calprotectin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Biophysical Examination of the Calcium-Modulated Nickel-Binding Properties of Human Calprotectin Reveals Conformational Change in the EF-Hand Domains and His3Asp Site.

Nakashige, T.G.Bowman, S.E.J.Zygiel, E.M.Drennan, C.L.Nolan, E.M.

(2018) Biochemistry 57: 4155-4164

  • DOI: 10.1021/acs.biochem.8b00415
  • Primary Citation of Related Structures:  
    6DS2

  • PubMed Abstract: 
  • Calprotectin (CP, S100A8/S100A9 oligomer, MRP-8/MRP-14 oligomer) is a host-defense protein that sequesters nutrient transition metals from microbes. Each S100A8/S100A9 heterodimer contains four EF-hand domains and two transition-metal-binding sites. ...

    Calprotectin (CP, S100A8/S100A9 oligomer, MRP-8/MRP-14 oligomer) is a host-defense protein that sequesters nutrient transition metals from microbes. Each S100A8/S100A9 heterodimer contains four EF-hand domains and two transition-metal-binding sites. We investigate the effect of Ca(II) ions on the structure and Ni(II)-binding properties of human CP. By employing energy dispersive X-ray (EDX) spectroscopy, we evaluate the metal content of Ni(II)-bound CP-Ser [oligomer of S100A8(C42S) and S100A9(C3S)] crystals obtained in the absence and presence of Ca(II). We present a 2.1 Å resolution crystal structure of Ni(II)-bound CP-Ser and compare this structure to a reported Ni(II)- and Ca(II)-bound CP-Ser structure [Nakashige, T. G., et al. (2017) J. Am. Chem. Soc. 139, 8828-8836]. This analysis reveals conformational changes associated with coordination of Ca(II) to the EF-hands of S100A9 and that Ca(II) binding affects the coordination number and geometry of the Ni(II) ion bound to the His 3 Asp site. In contrast, negligible differences are observed for the Ni(II)-His 6 site in the absence and presence of Ca(II). Biochemical studies show that, whereas the His 6 site has a thermodynamic preference for Ni(II) over Zn(II), the His 3 Asp site selects for Zn(II) over Ni(II), and relatively rapid metal exchange occurs at this site. These observations inform the working model for how CP withholds nutrient metals in the extracellular space.


    Organizational Affiliation

    Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-1393, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein S100-A8ACEG93Homo sapiensMutation(s): 1 
Gene Names: S100A8CAGACFAGMRP8
Find proteins for P05109 (Homo sapiens)
Explore P05109 
Go to UniProtKB:  P05109
NIH Common Fund Data Resources
PHAROS  P05109
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein S100-A9BDFH114Homo sapiensMutation(s): 0 
Gene Names: S100A9CAGBCFAGMRP14
Find proteins for P06702 (Homo sapiens)
Explore P06702 
Go to UniProtKB:  P06702
NIH Common Fund Data Resources
PHAROS  P06702
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download CCD File 
B, C, D, E, F, H
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, C, D, E, F, G
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.145α = 90
b = 78.082β = 90
c = 223.787γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1352132
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM126376
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM118695
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM069857

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence