5QU2

Crystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Small molecule AX-024 reduces T cell proliferation independently of CD3ε/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain.

Richter, K.Rufer, A.C.Muller, M.Burger, D.Casagrande, F.Grossenbacher, T.Huber, S.Hug, M.N.Koldewey, P.D'Osualdo, A.Schlatter, D.Stoll, T.Rudolph, M.G.

(2020) J Biol Chem 295: 7849-7864

  • DOI: 10.1074/jbc.RA120.012788
  • Primary Citation of Related Structures:  
    5QU2, 5QU1, 5QU4, 5QU3, 5QU6, 5QU5, 5QU8, 5QU7, 5QUA

  • PubMed Abstract: 
  • Activation of the T cell receptor (TCR) results in binding of the adapter protein Nck (noncatalytic region of tyrosine kinase) to the CD3ϵ subunit of the TCR. The interaction was suggested to be important for the amplification of TCR signals and is governed by a proline-rich sequence (PRS) in CD3ϵ that binds to the first Src homology 3 (SH3) domain of Nck (Nck-SH3 ...

    Activation of the T cell receptor (TCR) results in binding of the adapter protein Nck (noncatalytic region of tyrosine kinase) to the CD3ϵ subunit of the TCR. The interaction was suggested to be important for the amplification of TCR signals and is governed by a proline-rich sequence (PRS) in CD3ϵ that binds to the first Src homology 3 (SH3) domain of Nck (Nck-SH3.1). Inhibition of this protein/protein interaction ameliorated inflammatory symptoms in mouse models of multiple sclerosis, psoriasis, and asthma. A small molecule, AX-024, was reported to inhibit the Nck/CD3ϵ interaction by physically binding to the Nck1-SH3.1 domain, suggesting a route to develop an inhibitor of the Nck1/CD3ϵ interaction for modulating TCR activity in autoimmune and inflammatory diseases. We show here that AX-024 reduces T cell proliferation upon weak TCR stimulation but does not significantly affect phosphorylation of Zap70 (ζ chain of T cell receptor-associated protein kinase 70). We also find that AX-024 is likely not involved in modulating the Nck/TCR interaction but probably has other targets in T cells. An array of biophysical techniques did not detect a direct interaction between AX-024 and Nck-SH3.1 in vitro Crystal structures of the Nck-SH3.1 domain revealed its binding mode to the PRS in CD3ϵ. The SH3 domain tends to generate homodimers through a domain swap. Domain swaps observed previously in other SH3 domains indicate a general propensity of this protein fold to exchange structural elements. The swapped form of Nck-SH3.1 is unable to bind CD3ϵ, possibly representing an inactive form of Nck in cells.


    Organizational Affiliation

    Therapeutic Modalities, Lead Discovery and Medicinal Chemistry, pRED Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland markus.rudolph@roche.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytoplasmic protein NCK1A, B60Homo sapiensMutation(s): 0 
Gene Names: NCK1NCK
UniProt & NIH Common Fund Data Resources
Find proteins for P16333 (Homo sapiens)
Explore P16333 
Go to UniProtKB:  P16333
PHAROS:  P16333
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ACE-PRO-PRO-PRO-VAL-PRO-ASN-PRO-ASP-TYR-NH2C [auth D], D [auth E]11synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07766 (Homo sapiens)
Explore P07766 
Go to UniProtKB:  P07766
PHAROS:  P07766
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.65α = 90
b = 63.34β = 90
c = 99.68γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2019-12-13 
  • Released Date: 2020-02-12 
  • Deposition Author(s): Rudolph, M.G.

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 2.0: 2020-02-26
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2021-05-12
    Changes: Derived calculations, Structure summary
  • Version 2.2: 2021-06-30
    Changes: Database references