5ELI

Triggering receptor expressed on myeloid cells 2

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2015-11-04 Released: 2016-12-28 
  • Deposition Author(s): Brett, T.J., Kober, D.L.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Neurodegenerative disease mutations in TREM2 reveal a functional surface and distinct loss-of-function mechanisms.

Kober, D.L.Alexander-Brett, J.M.Karch, C.M.Cruchaga, C.Colonna, M.Holtzman, M.J.Brett, T.J.

(2016) Elife 5

  • DOI: 10.7554/eLife.20391
  • Primary Citation of Related Structures:  
    5ELI

  • PubMed Abstract: 
  • Genetic variations in the myeloid immune receptor TREM2 are linked to several neurodegenerative diseases. To determine how TREM2 variants contribute to these diseases, we performed structural and functional studies of wild-type and variant proteins. Our 3 ...

    Genetic variations in the myeloid immune receptor TREM2 are linked to several neurodegenerative diseases. To determine how TREM2 variants contribute to these diseases, we performed structural and functional studies of wild-type and variant proteins. Our 3.1 Å TREM2 crystal structure revealed that mutations found in Nasu-Hakola disease are buried whereas Alzheimer's disease risk variants are found on the surface, suggesting that these mutations have distinct effects on TREM2 function. Biophysical and cellular methods indicate that Nasu-Hakola mutations impact protein stability and decrease folded TREM2 surface expression, whereas Alzheimer's risk variants impact binding to a TREM2 ligand. Additionally, the Alzheimer's risk variants appear to epitope map a functional surface on TREM2 that is unique within the larger TREM family. These findings provide a guide to structural and functional differences among genetic variants of TREM2, indicating that therapies targeting the TREM2 pathway should be tailored to these genetic and functional differences with patient-specific medicine approaches for neurodegenerative disorders.


    Organizational Affiliation

    Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Triggering receptor expressed on myeloid cells 2 AB126Homo sapiensMutation(s): 0 
Gene Names: TREM2
Find proteins for Q9NZC2 (Homo sapiens)
Explore Q9NZC2 
Go to UniProtKB:  Q9NZC2
NIH Common Fund Data Resources
PHAROS:  Q9NZC2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 
  • Space Group: P 64 2 2
  • Diffraction Data DOI: 10.15785/SBGRID/415 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.763α = 90
b = 125.763β = 90
c = 183.659γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01-HL119813

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-04
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.3: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary