9PWN | pdb_00009pwn

Crystal structure of Fabs 7411 in complex with TREM2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.218 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9PWN

This is version 1.0 of the entry. See complete history

Literature

Building a potent TREM2 agonistic, biparatopic, common light chain antibody.

da Silva Almeida, A.Geddie, M.L.Bhate, A.Quan, C.Arndt, J.W.Jiao, Y.Santoro, J.C.Noiman, L.Vijayakumar, R.Sanchez-Salazar, J.Datta, A.Antognetti, G.Hartana, C.A.Wang, X.F.Smith, B.A.Bartlett, D.Duncan, D.Liu, C.C.Otero Gutierrez, K.Cameron, T.O.Koirala, S.Cooke, H.A.

(2025) MAbs 17: 2546554-2546554

  • DOI: https://doi.org/10.1080/19420862.2025.2546554
  • Primary Citation Related Structures: 
    9PWN, 9PX5

  • PubMed Abstract: 

    Triggering Receptor Expressed on Myeloid cells 2 (TREM2) plays an important role in microglial function and has been genetically linked to Alzheimer's disease. Activation of TREM2 signaling may contribute to protection against neurotoxic effects of amyloid. Numerous TREM2 activating antibodies have been shown to modulate downstream microglial functions to different degrees, with mixed results in preclinical models and in the clinic. We sought to generate an effectorless agonistic antibody that acted solely through TREM2 engagement with sufficient potency to activate TREM2 in the brain. Our approach focused on building a multivalent biparatopic TREM2 antibody that could mimic the higher order clustering induced by native polyanionic ligands of TREM2. We describe our screening strategy and findings that led to the discovery of a potential therapeutic molecule composed of antibodies selected for optimal affinity, binding epitopes, and geometry. The most productive antibody pair was selected from a common light chain yeast-display library, which required multiple rounds of affinity maturation. Lead antibody candidates were converted into asymmetric tetravalent bispecifics via controlled Fab-arm exchange and subsequently screened in signaling assays. The most productive antibody pair was reengineered into a symmetric tetravalent format, increasing potency and simplifying development. This molecule exhibited higher efficacy and potency in signaling assays than other antibody formats tested and elicited TREM2-mediated chemokine responses in vivo. Our results demonstrate a biparatopic strategy for producing a high potency TREM2 agonistic antibody with low effector function that can modulate TREM2 signaling in vitro and brain pharmacodynamic responses in vivo.


  • Organizational Affiliation
    • Biologics Drug Discovery, Biogen, Cambridge, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 49.9 kDa 
  • Atom Count: 3,629 
  • Modeled Residue Count: 445 
  • Deposited Residue Count: 451 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
7411 Fab Heavy ChainA [auth H]221Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
7411 Fab Light ChainB [auth L]212Homo sapiensMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
TREM-2 stalk peptideC [auth A]18Homo sapiensMutation(s): 0 
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
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
D [auth H]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H
I [auth H]
J [auth H]
K [auth H]
L [auth H]
H,
I [auth H],
J [auth H],
K [auth H],
L [auth H],
N [auth L],
O [auth L],
P [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth H],
F [auth H],
G [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
M [auth H],
Q [auth L],
R [auth L],
S [auth L]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.218 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.65α = 90
b = 71.76β = 90
c = 105.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release