6U6V

Crystal structure of human PD-1H / VISTA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

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This is version 1.3 of the entry. See complete history


Literature

Structural insight into T cell coinhibition by PD-1H (VISTA).

Slater, B.T.Han, X.Chen, L.Xiong, Y.

(2020) Proc Natl Acad Sci U S A 117: 1648-1657

  • DOI: https://doi.org/10.1073/pnas.1908711117
  • Primary Citation of Related Structures:  
    6U6V

  • PubMed Abstract: 

    Programmed death-1 homolog (PD-1H), a CD28/B7 family molecule, coinhibits T cell activation and is an attractive immunotherapeutic target for cancer and inflammatory diseases. The molecular basis of its function, however, is unknown. Bioinformatic analyses indicated that PD-1H has a very long Ig variable region (IgV)-like domain and extraordinarily high histidine content, suggesting that unique structural features may contribute to coinhibitory mechanisms. Here we present the 1.9-Å crystal structure of the human PD-1H extracellular domain. It reveals an elongated CC' loop and a striking concentration of histidine residues, located in the complementarity-determining region-like proximal half of the molecule. We show that surface-exposed histidine clusters are essential for robust inhibition of T cell activation. PD-1H exhibits a noncanonical IgV-like topology including an extra "H" β-strand and "clamping" disulfide, absent in known IgV-like structures, that likely restricts its orientation on the cell surface differently from other IgV-like domains. These results provide important insight into a molecular basis of T cell coinhibition by PD-1H.


  • Organizational Affiliation

    Department of Immunobiology, Yale University, New Haven, CT 06511.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V-type immunoglobulin domain-containing suppressor of T-cell activation174Homo sapiensMutation(s): 0 
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.821α = 90
b = 55.833β = 97.69
c = 42.271γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
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: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary