8SJC | pdb_00008sjc

Crystal structure of Zn2+ bound calprotectin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.197 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The C-terminal extension of calprotectin mediates zinc chelation and modulates Staphylococcus aureus biomass accumulation.

Perera, Y.R.Enriquez, K.T.Rodriguez, A.Garcia, V.Akizuki, T.Naretto, A.Togashi, M.Guillen, R.Skaar, E.P.Chazin, W.J.

(2025) Protein Sci 34: e70294-e70294

  • DOI: https://doi.org/10.1002/pro.70294
  • Primary Citation of Related Structures:  
    8SJC

  • PubMed Abstract: 

    Calprotectin (CP) is an S100A8/S100A9 heterodimer that plays an important role in nutritional immunity at the host-microbe interface. CP combats Staphylococcus aureus growth by sequestration of zinc and other trace transition metals; however, questions remain about whether CP antimicrobial activity strictly relies on metal sequestration. Moreover, the precise mechanism for how zinc binds at the two distinct transition metal binding sites of CP is not known. High-resolution X-ray crystal structures reveal tetracoordinate binding in the canonical His 3 Asp site and hexacoordinate binding in the His 6 site similar to the binding of manganese and nickel in this site. The S100A9 C-terminal extension (tail) contributes two of the His residues in the His 6 metal-binding site, but measurements of zinc affinity show there is no significant reduction upon mutation of these His residues or deletion of the entire C-terminal tail. Bacterial growth and static biofilm assays show that the His mutations affect S. aureus biomass accumulation differently than loss of the S100A9 C-terminal tail, despite resulting in the same defect in bacterial-CP binding. These results reveal that the S100A9 tail of CP has a role in preventing S. aureus biomass accumulation.


  • Organizational Affiliation
    • Departments of Biochemistry and Chemistry, Vanderbilt University, Nashville, Tennessee, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein S100-A8
A, B
87Homo sapiensMutation(s): 1 
Gene Names: S100A8CAGACFAGMRP8
UniProt & NIH Common Fund Data Resources
Find proteins for P05109 (Homo sapiens)
Explore P05109 
Go to UniProtKB:  P05109
PHAROS:  P05109
GTEx:  ENSG00000143546 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05109
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein S100-A9
C, D
108Homo sapiensMutation(s): 0 
Gene Names: S100A9CAGBCFAGMRP14
UniProt & NIH Common Fund Data Resources
Find proteins for P06702 (Homo sapiens)
Explore P06702 
Go to UniProtKB:  P06702
PHAROS:  P06702
GTEx:  ENSG00000163220 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06702
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
E [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
O [auth C],
R [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
K [auth C]
L [auth C]
F [auth A],
G [auth A],
I [auth B],
K [auth C],
L [auth C],
M [auth C],
N [auth C],
P [auth D],
Q [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth B],
J [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.611α = 90
b = 114.611β = 90
c = 53.182γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
Cootmodel building
PHENIXrefinement
HKL-2000data reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 AI127793
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesAI101171

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references, Structure summary