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 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9NZC2-1
Sequence Annotations
Expand
  • 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
  • Version 1.5: 2024-10-23
    Changes: Structure summary