5W1F

Crystal structure of Ni(II)- and Ca(II)-bound human calprotectin

  • Classification: METAL BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): 

  • Deposited: 2017-06-03 Released: 2017-06-14 
  • Deposition Author(s): Nakashige, T.G., Drennan, C.L., Nolan, E.M.
  • Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences; National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Center for Research Resources 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Nickel Sequestration by the Host-Defense Protein Human Calprotectin.

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

(2017) J. Am. Chem. Soc. 139: 8828-8836

  • DOI: 10.1021/jacs.7b01212

  • PubMed Abstract: 
  • The human innate immune protein calprotectin (CP, S100A8/S100A9 oligomer, calgranulin A/calgranulin B oligomer, MRP-8/MRP-14 oligomer) chelates a number of first-row transition metals, including Mn(II), Fe(II), and Zn(II), and can withhold these esse ...

    The human innate immune protein calprotectin (CP, S100A8/S100A9 oligomer, calgranulin A/calgranulin B oligomer, MRP-8/MRP-14 oligomer) chelates a number of first-row transition metals, including Mn(II), Fe(II), and Zn(II), and can withhold these essential nutrients from microbes. Here we elucidate the Ni(II) coordination chemistry of human CP. We present a 2.6-Å crystal structure of Ni(II)- and Ca(II)-bound CP, which reveals that CP binds Ni(II) ions at both its transition-metal-binding sites: the His3Asp motif (site 1) and the His6 motif (site 2). Further biochemical studies establish that coordination of Ni(II) at the hexahistidine site is thermodynamically preferred over Zn(II). We also demonstrate that CP can sequester Ni(II) from two human pathogens, Staphylococcus aureus and Klebsiella pneumoniae, that utilize this metal nutrient during infection, and inhibit the activity of the Ni(II)-dependent enzyme urease in bacterial cultures. In total, our findings expand the biological coordination chemistry of Ni(II)-chelating proteins in nature and provide a foundation for evaluating putative roles of CP in Ni(II) homeostasis at the host-microbe interface and beyond.


    Organizational Affiliation

    Department of Chemistry, ‡Department of Biology, and §Howard Hughes Medical Institute, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein S100-A8
A, C, G, E
93Homo sapiensMutation(s): 1 
Gene Names: S100A8 (CAGA, CFAG, MRP8)
Find proteins for P05109 (Homo sapiens)
Go to Gene View: S100A8
Go to UniProtKB:  P05109
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein S100-A9
B, D, H, F
114Homo sapiensMutation(s): 1 
Gene Names: S100A9 (CAGB, CFAG, MRP14)
Find proteins for P06702 (Homo sapiens)
Go to Gene View: S100A9
Go to UniProtKB:  P06702
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, E, G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
B, C, D, E, F, H
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.020α = 90.00
b = 77.611β = 90.00
c = 222.722γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesP30- ES002109
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM069857
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41 GM103403
National Institutes of Health/National Center for Research ResourcesUnited StatesS10 RR029205
National Institutes of Health/National Institute of General Medical SciencesUnited StatesHHSN272200700055C

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-21
    Type: Data collection, Database references
  • Version 1.2: 2017-07-19
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence