9I3P | pdb_00009i3p

CryoEM structure of the Themis:Grb2 complex with bound ProMacrobody 256


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
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wwPDB Validation 3D Report Full Report

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Literature

Structural and mechanistic insights into the constitutive Themis-Grb2 complex in T cell signalling.

Clancy, D.M.Sanz-Sanjuan, A.Gilis, E.Tougaard, P.Velghe, I.Van Droogenbroeck, Y.Felix, J.Bloch, Y.Cuadrado, A.F.Merceron, R.Schenck, S.Vandenabeele, P.Brunner, J.D.Taghon, T.Elewaut, D.Savvides, S.N.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-73359-8
  • Primary Citation Related Structures: 
    9I3P, 9IAZ

  • PubMed Abstract: 

    Thymocyte selection is essential for establishing the T cell repertoire, maintaining self-tolerance and preventing autoimmunity. Themis, the archetypal member of a metazoan protein family defined by CABIT domains, centrally regulates this process by integrating T cell receptor (TCR) signalling. Themis has been proposed to constitutively partner with the multifunctional adaptor Grb2, yet the structural and mechanistic basis of this assembly has remained enigmatic. Here, we use Cryo-EM to reveal how the tandem CABIT domains and proline-rich sequence of Themis cooperatively engulf the C-terminal SH3 domain of Grb2, while the unbound domains of Grb2 remain poised to recruit additional binding partners. Furthermore, we uncover inherent interdomain flexibility in unbound Themis that resolves upon Grb2 binding. Structure-guided mutations abrogate the Themis-Grb2 interaction and fail to regulate the tyrosine phosphatase SHP-1 after TCR stimulation, recapitulating the phenotype of Themis-deficient cells. Our findings define the Themis-Grb2 complex as a dynamic structural hub in T cell signalling.


  • Organizational Affiliation
    • Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium. danielle.clancy@irc.vib-ugent.be.

Macromolecule Content 

  • Total Structure Weight: 143.78 kDa 
  • Atom Count: 8,285 
  • Modeled Residue Count: 1,040 
  • Deposited Residue Count: 1,265 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Growth factor receptor-bound protein 2224Homo sapiensMutation(s): 0 
Gene Names: GRB2ASH
UniProt & NIH Common Fund Data Resources
Find proteins for P62993 (Homo sapiens)
Explore P62993 
Go to UniProtKB:  P62993
PHAROS:  P62993
GTEx:  ENSG00000177885 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62993
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein THEMIS563Homo sapiensMutation(s): 0 
Gene Names: THEMISC6orf190C6orf207
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N1K5 (Homo sapiens)
Explore Q8N1K5 
Go to UniProtKB:  Q8N1K5
PHAROS:  Q8N1K5
GTEx:  ENSG00000172673 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N1K5
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ProMacrobody 256478synthetic constructEscherichia coli
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Explore P0AEY0 
Go to UniProtKB:  P0AEY0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEY0
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseD [auth E]2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)Belgium1219923N
Research Foundation - Flanders (FWO)BelgiumG049820N

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-29
    Type: Initial release
  • Version 1.1: 2026-06-03
    Changes: Data collection, Database references