Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 6 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 243.40 kDa 
• Atom Count: 15730 
• Modelled Residue Count: 2047 
• Deposited Residue Count: 2220 
• Unique protein chains: 2

6YMQ

TREM2 extracellular domain (19-131) in complex with single-chain variable 4 (scFv-4)

• DOI: 10.2210/pdb6YMQ/pdb

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


• Deposited: 2020-04-09 Released: 2021-02-17 
• Deposition Author(s): Szykowska, A., Preger, C., Scacioc, A., Mukhopadhyay, S.M.M., McKinley, G., Graslund, S., Wigren, E., Persson, H., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Di Daniel, E., Davis, J.B., Burgess-Brown, N., Bullock, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.07 Å
• R-Value Free: 0.288 
• R-Value Work: 0.274 
• R-Value Observed: 0.274 

Literature

Selection and structural characterisation 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., 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) Biorxiv 

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-chain variable 4	A, B, C, D, E, F	245	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Triggering receptor expressed on myeloid cells 2	D000, G, H, I, J, K	125	Homo sapiens	Mutation(s): 0  Gene Names: TREM2
Find proteins for Q9NZC2 (Homo sapiens) Explore Q9NZC2  Go to UniProtKB:  Q9NZC2
NIH Common Fund Data Resources
PHAROS:  Q9NZC2 GTEx:  ENSG00000095970

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D000, G, H, I, J, K	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPD	J	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GLY	G	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.07 Å
• R-Value Free: 0.288 
• R-Value Work: 0.274 
• R-Value Observed: 0.274 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.51	α = 90
b = 180.77	β = 90
c = 125.51	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-04-09 
• Released Date: 2021-02-17 
Deposition Author(s): Szykowska, A., Preger, C., Scacioc, A., Mukhopadhyay, S.M.M., McKinley, G., Graslund, S., Wigren, E., Persson, H., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Di Daniel, E., Davis, J.B., Burgess-Brown, N., Bullock, A.

Revision History  

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