7QUV

Crystal structure of human Calprotectin (S100A8/S100A9) in complex with Peptide 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.226 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

High-affinity peptides developed against calprotectin and their application as synthetic ligands in diagnostic assays.

Diaz-Perlas, C.Ricken, B.Farrera-Soler, L.Guschin, D.Pojer, F.Lau, K.Gerhold, C.B.Heinis, C.

(2023) Nat Commun 14: 2774-2774

  • DOI: https://doi.org/10.1038/s41467-023-38075-7
  • Primary Citation of Related Structures:  
    7QUV

  • PubMed Abstract: 

    Common inflammatory disorders such as ulcerative colitis and Crohn's disease are non-invasively diagnosed or monitored by the biomarker calprotectin. However, current quantitative tests for calprotectin are antibody-based and vary depending on the type of antibody and assay used. Additionally, the binding epitopes of applied antibodies are not characterized by structures and for most antibodies it is unclear if they detect calprotectin dimer, tetramer, or both. Herein, we develop calprotectin ligands based on peptides, that offer advantages such as homogenous chemical composition, heat-stability, site-directed immobilization, and chemical synthesis at high purity and at low cost. By screening a 100-billion peptide phage display library against calprotectin, we identified a high-affinity peptide (K d  = 26 ± 3 nM) that binds to a large surface region (951 Å 2 ) as shown by X-ray structure analysis. The peptide uniquely binds the calprotectin tetramer, which enabled robust and sensitive quantification of a defined species of calprotectin by ELISA and lateral flow assays in patient samples, and thus offers an ideal affinity reagent for next-generation inflammatory disease diagnostic assays.


  • Organizational Affiliation

    Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein S100-A9A [auth B]122Homo sapiensMutation(s): 1 
Gene Names: S100A9CAGBCFAGMRP14
UniProt & NIH Common Fund Data Resources
Find proteins for P06702 (Homo sapiens)
Explore P06702 
Go to UniProtKB:  P06702
GTEx:  ENSG00000163220 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06702
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein S100-A8B [auth A]95Homo sapiensMutation(s): 1 
Gene Names: S100A8CAGACFAGMRP8
UniProt & NIH Common Fund Data Resources
Find proteins for P05109 (Homo sapiens)
Explore P05109 
Go to UniProtKB:  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:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide 318synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F3U (Subject of Investigation/LOI)
Query on F3U

Download Ideal Coordinates CCD File 
M [auth C]4-methanoyl-2-(6-oxidanyl-3-oxidanylidene-4~{H}-xanthen-9-yl)benzoic acid
C21 H12 O6
CYKLSLGBUUWGRE-UHFFFAOYSA-N
PGE
Query on PGE

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G [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL
Query on GOL

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H [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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L [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
Query on NI

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F [auth B]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CA
Query on CA

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D [auth B],
E [auth B],
I [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

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K [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA
Query on NA

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J [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
NH2
Query on NH2

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N [auth C]AMINO GROUP
H2 N
QGZKDVFQNNGYKY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.226 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.789α = 90
b = 50.789β = 90
c = 148.752γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-02-07
    Changes: Refinement description