6XDS

Crystal structure of MBP-TREM2 Ig domain fusion with fragment, 2-((4-bromophenyl)amino)ethan-1-ol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Development of a robust crystallization platform for immune receptor TREM2 using a crystallization chaperone strategy.

Byrne, N.J.Lee, A.C.Kostas, J.Reid, J.C.Partridge, A.T.So, S.S.Cowan, J.E.Abeywickrema, P.Huang, H.Zebisch, M.Barker, J.J.Soisson, S.M.Brooun, A.Su, H.P.

(2021) Protein Expr Purif 179: 105796-105796

  • DOI: 10.1016/j.pep.2020.105796
  • Primary Citation of Related Structures:  
    6XDS

  • PubMed Abstract: 
  • TREM2 has been identified by genomic analysis as a potential and novel target for the treatment of Alzheimer's disease. To enable structure-based screening of potential small molecule therapeutics, we sought to develop a robust crystallization platform for the TREM2 Ig-like domain ...

    TREM2 has been identified by genomic analysis as a potential and novel target for the treatment of Alzheimer's disease. To enable structure-based screening of potential small molecule therapeutics, we sought to develop a robust crystallization platform for the TREM2 Ig-like domain. A systematic set of constructs containing the structural chaperone, maltose binding protein (MBP), fused to the Ig domain of TREM2, were evaluated in parallel expression and purification, followed by crystallization studies. Using protein crystallization and high-resolution diffraction as a readout, a MBP-TREM2 Ig fusion construct was identified that generates reproducible protein crystals diffracting at 2.0 Å, which makes it suitable for soaking of potential ligands. Importantly, analysis of crystal packing interfaces indicates that most of the surface of the TREM2 Ig domain is available for small molecule binding. A proof of concept co-crystallization study with a small library of fragments validated potential utility of this system for the discovery of new TREM2 therapeutics.


    Organizational Affiliation

    Department of Computational and Structural Sciences, Merck & Co., Inc., West Point, PA, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sugar ABC transporter substrate-binding protein,Triggering receptor expressed on myeloid cells 2 A492Methanosarcina mazeiHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malEDU74_04045TREM2
Find proteins for A0A0F8NYV9 (Methanosarcina mazei)
Explore A0A0F8NYV9 
Go to UniProtKB:  A0A0F8NYV9
Find proteins for Q9NZC2 (Homo sapiens)
Explore Q9NZC2 
Go to UniProtKB:  Q9NZC2
NIH Common Fund Data Resources
PHAROS:  Q9NZC2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
3 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V5S
Query on V5S

Download Ideal Coordinates CCD File 
A
2-[(4-bromophenyl)amino]ethan-1-ol
C8 H10 Br N O
GYWMAZOWKOVMKS-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900009
Query on PRD_900009
Balpha-maltotrioseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.84α = 90
b = 80.35β = 90
c = 103.89γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2020-06-11 
  • Released Date: 2021-02-17 
  • Deposition Author(s): Su, H.P.

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release