6Y6C

TREM2 extracellular domain (19-174) in complex with single-chain variable fragment (scFv-4)

• PDB DOI: https://doi.org/10.2210/pdb6Y6C/pdb

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


• Deposited: 2020-02-26 Released: 2021-02-17 
• Deposition Author(s): Szykowska, A., Preger, C., Williams, E., Mukhopadhyay, S.M.M., McKinley, G., Gruslund, S., Wigren, E., Persson, H., Arrowsmith, C.H., Edwards, A., von Delft, F., Bountra, C., Davis, J.B., Di Daniel, E., Burgess-Brown, N., Bullock, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.216 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.32 kDa 
• Atom Count: 5,771 
• Modelled Residue Count: 693 
• Deposited Residue Count: 894 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triggering receptor expressed on myeloid cells 2	A, B	202	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Single chain variable	C, D	245	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.216 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.661	α = 90
b = 111.661	β = 90
c = 232.196	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PHENIX	data processing
Coot	model building
xia2	data processing
xia2	data reduction
DIALS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Szykowska, A., Preger, C., Williams, E., Mukhopadhyay, S.M.M., McKinley, G., Gruslund, S., Wigren, E., Persson, H., Arrowsmith, C.H., Edwards, A., von Delft, F., Bountra, C., Davis, J.B., Di Daniel, E., Burgess-Brown, N., Bullock, A.

Revision History  

• 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, Source and taxonomy
• Version 1.4: 2024-01-31
  Changes: Data collection, Refinement description