6MVL | pdb_00006mvl

Crystal structure of VISTA bound to a pH-selective antibody Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 
    0.225 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6MVL

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

VISTA is an acidic pH-selective ligand for PSGL-1.

Johnston, R.J.Su, L.J.Pinckney, J.Critton, D.Boyer, E.Krishnakumar, A.Corbett, M.Rankin, A.L.Dibella, R.Campbell, L.Martin, G.H.Lemar, H.Cayton, T.Huang, R.Y.Deng, X.Nayeem, A.Chen, H.Ergel, B.Rizzo, J.M.Yamniuk, A.P.Dutta, S.Ngo, J.Shorts, A.O.Ramakrishnan, R.Kozhich, A.Holloway, J.Fang, H.Wang, Y.K.Yang, Z.Thiam, K.Rakestraw, G.Rajpal, A.Sheppard, P.Quigley, M.Bahjat, K.S.Korman, A.J.

(2019) Nature 574: 565-570

  • DOI: https://doi.org/10.1038/s41586-019-1674-5
  • Primary Citation Related Structures: 
    6MVL

  • PubMed Abstract: 

    Co-inhibitory immune receptors can contribute to T cell dysfunction in patients with cancer 1,2 . Blocking antibodies against cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and programmed cell death 1 (PD-1) partially reverse this effect and are becoming standard of care in an increasing number of malignancies 3 . However, many of the other axes by which tumours become inhospitable to T cells are not fully understood. Here we report that V-domain immunoglobulin suppressor of T cell activation (VISTA) engages and suppresses T cells selectively at acidic pH such as that found in tumour microenvironments. Multiple histidine residues along the rim of the VISTA extracellular domain mediate binding to the adhesion and co-inhibitory receptor P-selectin glycoprotein ligand-1 (PSGL-1). Antibodies engineered to selectively bind and block this interaction in acidic environments were sufficient to reverse VISTA-mediated immune suppression in vivo. These findings identify a mechanism by which VISTA may engender resistance to anti-tumour immune responses, as well as an unexpectedly determinative role for pH in immune co-receptor engagement.


  • Organizational Affiliation
    • Immuno-Oncology Discovery, Bristol-Myers Squibb, Redwood City, CA, USA. robert.johnston@bms.com.

Macromolecule Content 

  • Total Structure Weight: 68.4 kDa 
  • Atom Count: 5,135 
  • Modeled Residue Count: 568 
  • Deposited Residue Count: 613 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
V-type immunoglobulin domain-containing suppressor of T-cell activation169Homo sapiensMutation(s): 3 
Gene Names: VSIRC10orf54SISP1VISTAPP2135UNQ730/PRO1412
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7M9 (Homo sapiens)
Explore Q9H7M9 
Go to UniProtKB:  Q9H7M9
PHAROS:  Q9H7M9
GTEx:  ENSG00000107738 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7M9
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9H7M9-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody Fab fragment heavy chainB [auth H]229Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody Fab fragment light chainC [auth L]215Homo sapiensMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth H]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth H],
J [auth H],
K [auth H],
L [auth H],
M [auth H],
N [auth H],
O [auth L],
P [auth L],
Q [auth L],
R [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free:  0.225 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.166α = 90
b = 125.856β = 90
c = 192.04γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Structure summary