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): Yes 

  • 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 (NIH/NIEHS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  
    5W1F

  • 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 essential nutrients from microbes ...

    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 His 3 Asp motif (site 1) and the His 6 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein S100-A8 ACEG93Homo 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein S100-A9 BDFH114Homo sapiensMutation(s): 1 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

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

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

Download Ideal Coordinates CCD File 
A, B, C, E, G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.02α = 90
b = 77.611β = 90
c = 222.722γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesP30- ES002109
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM069857
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103403
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10 RR029205
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesHHSN272200700055C

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Data collection, Database references
  • Version 1.2: 2017-07-19
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence