9GWZ | pdb_00009gwz

Crystal structure of 23ME-00610 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.256 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.222 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9GWZ

This is version 1.0 of the entry. See complete history

Literature

CD200R1 immune checkpoint blockade by the first-in-human anti-CD200R1 antibody 23ME-00610: molecular mechanism and engineering of a surrogate antibody.

Melero, C.Budiardjo, S.J.Daruwalla, A.Larrabee, L.Ganichkin, O.Heiler, A.J.Fenaux, J.Chung, B.Fuh, G.Huang, Y.M.

(2024) MAbs 16: 2410316-2410316

  • DOI: https://doi.org/10.1080/19420862.2024.2410316
  • Primary Citation Related Structures: 
    9GWT, 9GWZ

  • PubMed Abstract: 

    Human CD200R1 (hCD200R1), an immune inhibitory receptor expressed predominantly on T cells and myeloid cells, was identified as a promising immuno-oncology target by the 23andMe database. Blockade of CD200R1-dependent signaling enhances T cell-mediated antitumor activity in vitro and in vivo. 23ME-00610 is a potential first-in-class, humanized IgG1 investigational antibody that binds hCD200R1 with high affinity. We have previously shown that 23ME-00610 inhibits the hCD200R1 immune checkpoint function. Herein, we dissect the molecular mechanism of 23ME-00610 blockade of hCD200R1 by solving the crystal structure of 23ME-00610 Fab in complex with hCD200R1 and performing mutational studies, which show 23ME-00610 blocks the interaction between hCD200 and hCD200R1 through steric hindrance. However, 23ME-00610 does not bind CD200R1 of preclinical species such as cynomolgus monkey MfCD200R1. To enable preclinical toxicology studies of CD200R1 blockade in a pharmacologically relevant non-clinical species, we engineered a surrogate antibody with high affinity toward MfCD200R1. We used phage display libraries of 23ME-00610 variants with individual CDR residues randomized to all 20 amino acids, from which we identified mutations that switched on MfCD200R1 binding. Structural analysis suggests how the surrogate, named 23ME-00611, acquires the ortholog binding ability at the equivalent epitope of 23ME-00610. This engineering approach does not require a priori knowledge of structural and functional mapping of antibody-antigen interaction and thus is generally applicable for therapeutic antibody development when desired ortholog binding is lacking. These findings provide foundational insights as 23ME-00610 advances in clinical studies to gain understanding of the hCD200R1 immune checkpoint as a target in immuno-oncology.


  • Organizational Affiliation
    • 23andMe, Therapeutic Unit, South San Francisco, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 196.64 kDa 
  • Atom Count: 14,124 
  • Modeled Residue Count: 1,731 
  • Deposited Residue Count: 1,808 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
23ME-00610 Fab (heavy)A [auth HHH],
C [auth AAA],
E [auth CCC],
G [auth EEE]
234Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
23ME-00610 Fab (light)B [auth LLL],
D [auth BBB],
F [auth DDD],
H [auth FFF]
218Homo sapiensMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD

Query on MPD



Download:Ideal Coordinates CCD File
K [auth HHH],
P [auth BBB],
S [auth CCC]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
J [auth HHH]
N [auth AAA]
R [auth CCC]
T [auth CCC]
W [auth EEE]
J [auth HHH],
N [auth AAA],
R [auth CCC],
T [auth CCC],
W [auth EEE],
X [auth EEE]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth HHH]
L [auth HHH]
M [auth AAA]
O [auth AAA]
Q [auth CCC]
I [auth HHH],
L [auth HHH],
M [auth AAA],
O [auth AAA],
Q [auth CCC],
U [auth CCC],
V [auth EEE]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.256 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.222 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.274α = 90
b = 67.447β = 101.71
c = 136.88γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

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: 2024-10-23
    Type: Initial release