7S13 | pdb_00007s13

Crystal structure of Fab in complex with mouse CD96 dimer

• PDB DOI: https://doi.org/10.2210/pdb7S13/pdb

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


• Deposited: 2021-08-31 Released: 2021-10-20 
• Deposition Author(s): Lee, P.S., Barman, I., Strop, P.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.265 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Models: experimental

Literature

Antibody blockade of CD96 by distinct molecular mechanisms.

Lee, P.S., Chau, B., Barman, I., Bee, C., Jashnani, A., Hogan, J.M., Aguilar, B., Dollinger, G., Rajpal, A., Strop, P.

(2021) MAbs 13: 1979800-1979800

• PubMed: 34595996 
• DOI: https://doi.org/10.1080/19420862.2021.1979800
• Primary Citation Related Structures: 
  7S11, 7S13


• PubMed Abstract: 
  

  The molecular interactions of mouse CD96 to CD155 ligand and to two surrogate antibodies have been investigated. Biophysical and structural studies demonstrate that CD96 forms a homodimer but assembles as 1:1 heterodimeric complexes with CD155 or with one of the surrogate antibodies, which compete for the same binding interface. In comparison, the other surrogate antibody binds across the mouse CD96 dimer and recognizes a quaternary epitope spanning both protomers to block exposure of the ligand-binding site. This study reveals different blocking mechanisms and modalities of these two antibodies and may provide insight into the functional effects of antibodies against CD96.

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Organizational Affiliation: 
• Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, CA, USA.
Therapeutic Discovery, 3T Biosciences, South San Francisco, Ca, USA.
Discovery Biology, Frontier Medicines, South San Francisco, CA, USA.
Large Molecule Drug Discovery, Genentech Research and Early Development, South San Francisco, Ca, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 124.58 kDa 
• Atom Count: 8,274 
• Modeled Residue Count: 1,065 
• Deposited Residue Count: 1,128 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	A [auth H], C [auth I]	226	Rattus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	B [auth L], D [auth M]	213	Rattus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface protein tactile	E [auth C], F [auth D]	125	Mus musculus	Mutation(s): 0  Gene Names: Cd96
UniProt & NIH Common Fund Data Resources
Find proteins for Q3U0X8 (Mus musculus) Explore Q3U0X8  Go to UniProtKB:  Q3U0X8
IMPC:  MGI:1934368
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q3U0X8-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	K [auth C], L [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
FLC	J [auth I]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
EDO	G [auth H], H [auth L], I [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth H], C [auth I]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.265 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.03	α = 90
b = 131.25	β = 90
c = 186.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-20 
Deposition Author(s): Lee, P.S., Barman, I., Strop, P.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2021-10-20
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary