6YYE

TREM2 extracellular domain (19-131) in complex with single-chain variable fragment (scFv-2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.298 
  • R-Value Observed: 0.300 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Selection and structural characterization of anti-TREM2 scFvs that reduce levels of shed ectodomain.

Szykowska, A.Chen, Y.Smith, T.B.Preger, C.Yang, J.Qian, D.Mukhopadhyay, S.M.Wigren, E.Neame, S.J.Graslund, S.Persson, H.Atkinson, P.J.Di Daniel, E.Mead, E.Wang, J.Davis, J.B.Burgess-Brown, N.A.Bullock, A.N.

(2021) Structure 29: 1241-1252.e5

  • DOI: https://doi.org/10.1016/j.str.2021.06.010
  • Primary Citation of Related Structures:  
    6Y6C, 6YMQ, 6YYE

  • PubMed Abstract: 

    Mutations in TREM2, a receptor expressed by microglia in the brain, are associated with an increased risk of neurodegeneration, including Alzheimer's disease. Numerous studies support a role for TREM2 in sensing damaging stimuli and triggering signaling cascades necessary for neuroprotection. Despite its significant role, ligands and regulators of TREM2 activation, and the mechanisms governing TREM2-dependent responses and its cleavage from the membrane, remain poorly characterized. Here, we present phage display generated antibody single-chain variable fragments (scFvs) to human TREM2 immunoglobulin-like domain. Co-crystal structures revealed the binding of two scFvs to an epitope on the TREM2 domain distal to the putative ligand-binding site. Enhanced functional activity was observed for oligomeric scFv species, which inhibited the production of soluble TREM2 in a HEK293 cell model. We hope that detailed characterization of their epitopes and properties will facilitate the use of these renewable binders as structural and functional biology tools for TREM2 research.


  • Organizational Affiliation

    Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Triggering receptor expressed on myeloid cells 2
A, B
116Homo sapiensMutation(s): 0 
Gene Names: TREM2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZC2 (Homo sapiens)
Explore Q9NZC2 
Go to UniProtKB:  Q9NZC2
PHAROS:  Q9NZC2
GTEx:  ENSG00000095970 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZC2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TREM2 Single chain variable 2
C, D
247Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.298 
  • R-Value Observed: 0.300 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.942α = 90
b = 126.201β = 90
c = 225.007γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references
  • Version 1.2: 2021-11-17
    Changes: Data collection, Database references
  • Version 1.3: 2022-12-21
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description