8TBQ

The crystal structure of human VISTA extra cellular domain in complex with Fab fragment of pH-selective anti-VISTA antibody

• PDB DOI: https://doi.org/10.2210/pdb8TBQ/pdb

• Classification: PROTEIN BINDING,IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Homo sapiens
• Mutation(s): No 


• Deposited: 2023-06-29 Released: 2024-03-20 
• Deposition Author(s): van der Horst, E.H., Mukherjee, A., Thisted, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.291 
• R-Value Work: 0.237 

Literature

The pH-selective anti-VISTA antibody SNS-101 displays a favorable pharmacokinetic and safety profile and promotes anti-tumoral M1 macrophage polarization in PD-1 refractory settings

Thisted, T., Smith, F.D., Zhang, G., Feng, F., Kleschenko, Y., Mukherjee, A., Jiang, Z., Malhotra, K., Biesova, Z., Onumajuru, A., Gaelle, M., Takeuchi, Y., Thiam, K., Schreiber, R.D., van der Horst, E.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 132.21 kDa 
• Atom Count: 8,552 
• Modelled Residue Count: 1,135 
• Deposited Residue Count: 1,206 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SNS-101 Fab heavy chain	A [auth H], D [auth A]	229	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SNS-101 Fab light chain	B [auth L], E [auth B]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type immunoglobulin domain-containing suppressor of T-cell activation	C [auth P], F [auth Q]	159	Homo sapiens	Mutation(s): 0  Gene Names: VSIR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7M9 (Homo sapiens) Explore Q9H7M9  Go to UniProtKB:  Q9H7M9
PHAROS:  Q9H7M9 GTEx:  ENSG00000107738

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth P], J [auth Q], K [auth Q]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	G [auth H], H	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.291 
• R-Value Work: 0.237 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.659	α = 90
b = 39.512	β = 117.121
c = 177.979	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): van der Horst, E.H., Mukherjee, A., Thisted, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release