8S6Z | pdb_00008s6z

CD28 in complex with the antibody Fab fragment AI3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 
    0.258 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.197 (DCC) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8S6Z

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

NI-3201 Is a Bispecific Antibody Mediating PD-L1-Dependent CD28 Co-stimulation on T Cells for Enhanced Tumor Control.

Majocchi, S.Lloveras, P.Nouveau, L.Legrand, M.Viandier, A.Malinge, P.Charreton, M.Raymond, C.Pace, E.A.Millard, B.L.Svensson, L.A.Kelpsas, V.Anceriz, N.Salgado-Pires, S.Daubeuf, B.Magistrelli, G.Gueneau, F.Moine, V.Masternak, K.Shang, L.Fischer, N.Ferlin, W.G.

(2025) Cancer Immunol Res 13: 365-383

  • DOI: https://doi.org/10.1158/2326-6066.CIR-24-0298
  • Primary Citation Related Structures: 
    8S6Z

  • PubMed Abstract: 

    Despite advances in cancer immunotherapy, such as targeting the PD-1/PD-L1 axis, a substantial number of patients harbor tumors that are resistant or relapse. Selective engagement of T-cell co-stimulatory molecules with bispecific antibodies may offer novel therapeutic options by enhancing signal 1-driven activation occurring via T-cell receptor engagement. In this study, we report the development and preclinical characterization of NI-3201, a PD-L1×CD28 bispecific antibody generated on the κλ-body platform that was designed to promote T-cell activity and antitumor function through a dual mechanism of action. We confirmed that NI-3201 blocks the PD-L1/PD-1 immune checkpoint pathway and conditionally provides T-cell co-stimulation via CD28 (signal 2) when engaging PD-L1+ tumors or immune cells. In systems with signal 1-primed T cells, NI-3201 enhanced potent effector functionality: in vitro through antigen-specific recall assays with cytomegalovirus-specific T cells and in vivo by inducing tumor regression and immunologic memory in tumor-associated antigen-expressing MC38 syngeneic mouse models. When T-cell engagers were used to provide synthetic signal 1, the combination with NI-3201 resulted in synergistic T cell-dependent cytotoxicity and potent antitumor activity in two humanized mouse tumor models. Nonhuman primate safety assessments showed favorable tolerability and pharmacokinetics at pharmacologically active doses. Quantitative systems pharmacology modeling predicted that NI-3201 exposure results in antitumor activity in patients, but this remains to be investigated. Overall, this study suggests that by combining PD-L1 blockade with safe and effective CD28 co-stimulation, NI-3201 has the potential to improve cancer immunotherapy outcomes, and the clinical development of NI-3201 for PD-L1+ solid tumors is planned.


  • Organizational Affiliation
    • Light Chain Bioscience - Novimmune SA, Geneva, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 130.83 kDa 
  • Atom Count: 8,785 
  • Modeled Residue Count: 1,110 
  • Deposited Residue Count: 1,154 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain Fab fragment of AI3 antibody
A, D
223Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of AI3 antibody
B, E
220Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell-specific surface glycoprotein CD28
C, F
134Homo sapiensMutation(s): 0 
Gene Names: CD28
UniProt & NIH Common Fund Data Resources
Find proteins for P10747 (Homo sapiens)
Explore P10747 
Go to UniProtKB:  P10747
PHAROS:  P10747
GTEx:  ENSG00000178562 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10747
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P10747-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth F]
BA [auth C]
WA [auth F]
X [auth C]
AA [auth C],
AB [auth F],
BA [auth C],
WA [auth F],
X [auth C],
XA [auth F],
Y [auth C],
YA [auth F],
ZA [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
GA [auth D]
HA [auth D]
I [auth A]
LA [auth E]
M [auth B]
GA [auth D],
HA [auth D],
I [auth A],
LA [auth E],
M [auth B],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
BB [auth F]
CA [auth C]
FA [auth D]
H [auth A]
KA [auth E]
BB [auth F],
CA [auth C],
FA [auth D],
H [auth A],
KA [auth E],
N [auth B],
O [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN

Query on ZN



Download:Ideal Coordinates CCD File
CB [auth F]
DA [auth C]
EA [auth C]
IA [auth D]
J [auth A]
CB [auth F],
DA [auth C],
EA [auth C],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
L [auth A],
MA [auth E],
NA [auth E],
OA [auth E],
P [auth B],
PA [auth E],
Q [auth B],
QA [auth E],
R [auth B],
RA [auth E],
S [auth B],
SA [auth E],
T [auth B],
TA [auth E],
U [auth B],
UA [auth E],
V [auth B],
VA [auth E],
W [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free:  0.258 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.874α = 90
b = 117.939β = 90
c = 145.719γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
EDNAdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Database references
  • Version 1.2: 2025-01-22
    Changes: Database references, Derived calculations
  • Version 1.3: 2025-03-12
    Changes: Database references