8FWH | pdb_00008fwh

Crystal structure of bivalent antibody Fab fragment of Anti-human LAG3 (22D2)

• PDB DOI: https://doi.org/10.2210/pdb8FWH/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-01-22 Released: 2023-09-06 
• Deposition Author(s): Mishra, A.K., Agnihotri, P., Mariuzza, R.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.277 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 

Starting Model: experimental

Literature

CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3 determined using a bivalent Fab as fiducial marker.

Mishra, A.K., Shahid, S., Karade, S.S., Agnihotri, P., Kolesnikov, A., Hasan, S.S., Mariuzza, R.A.

(2023) Structure 31: 1149

• PubMed: 37619561 
• DOI: https://doi.org/10.1016/j.str.2023.07.013
• Primary Citation of Related Structures:  
  6WKM, 8FWH, 8SO3, 8SR0


• PubMed Abstract: 
  

  Lymphocyte activation gene 3 protein (LAG3) is an inhibitory receptor that is upregulated on exhausted T cells in tumors. LAG3 is a major target for cancer immunotherapy with many anti-LAG3 antibodies in clinical trials. However, there is no structural information on the epitopes recognized by these antibodies. We determined the single-particle cryoEM structure of a therapeutic antibody (favezelimab) bound to LAG3 to 3.5 Å resolution, revealing that favezelimab targets the LAG3-binding site for MHC class II, its canonical ligand. The small size of the complex between the conventional (monovalent) Fab of favezelimab and LAG3 (∼100 kDa) presented a challenge for cryoEM. Accordingly, we engineered a bivalent version of Fab favezelimab that doubled the size of the Fab-LAG3 complex and conferred a highly identifiable shape to the complex that facilitated particle selection and orientation for image processing. This study establishes bivalent Fabs as new fiducial markers for cryoEM analysis of small proteins.

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Organizational Affiliation: 
• W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, Baltimore, MD 21201, USA; Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Rockville, MD 20850, USA.
W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.71 kDa 
• Atom Count: 3,183 
• Modeled Residue Count: 429 
• Deposited Residue Count: 441 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-human LAG3 (22D2) heavy chain	A [auth HHH]	223	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-human LAG3 (22D2) light chain	B [auth LLL]	218	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO (Subject of Investigation/LOI)	C [auth LLL]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.277 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.287	α = 90
b = 44.39	β = 106.136
c = 89.084	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-06 
Deposition Author(s): Mishra, A.K., Agnihotri, P., Mariuzza, R.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI144422

Revision History  

• Version 1.0: 2023-09-06
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Structure summary