6NYP | pdb_00006nyp

Crystal structure of UL144/BTLA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.277 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure of human cytomegalovirus UL144, an HVEM orthologue, bound to the B and T cell lymphocyte attenuator.

Bitra, A.Nemcovicova, I.Picarda, G.Doukov, T.Wang, J.Benedict, C.A.Zajonc, D.M.

(2019) J Biological Chem 294: 10519-10529

  • DOI: https://doi.org/10.1074/jbc.RA119.009199
  • Primary Citation Related Structures: 
    6NYP

  • PubMed Abstract: 

    Human cytomegalovirus (HCMV) is a β-herpesvirus that has co-evolved with the host immune system to establish lifelong persistence. HCMV encodes many immunomodulatory molecules, including the glycoprotein UL144. UL144 is a structural mimic of the tumor necrosis factor receptor superfamily member HVEM (herpesvirus entry mediator), which binds to the various ligands LIGHT, LTα, BTLA, CD160, and gD. However, in contrast to HVEM, UL144 only binds BTLA, inhibiting T-cell activation. Here, we report the crystal structure of the UL144-BTLA complex, revealing that UL144 utilizes residues from its N-terminal cysteine-rich domain 1 (CRD1) to interact uniquely with BTLA. The shorter CRD2 loop of UL144 also alters the relative orientation of BTLA binding with both N-terminal CRDs. By employing structure-guided mutagenesis, we have identified a mutant of BTLA (L123A) that interferes with HVEM binding but preserves UL144 interactions. Furthermore, our results illuminate structural differences between UL144 and HVEM that explain its binding selectivity and highlight it as a suitable scaffold for designing superior, immune inhibitory BTLA agonists.


  • Organizational Affiliation
    • From the Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, California 92037.

Macromolecule Content 

  • Total Structure Weight: 103.36 kDa 
  • Atom Count: 5,508 
  • Modeled Residue Count: 696 
  • Deposited Residue Count: 900 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
B- and T-lymphocyte attenuator
A, B, C, D
107Homo sapiensMutation(s): 0 
Gene Names: BTLA
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z6A9 (Homo sapiens)
Explore Q7Z6A9 
Go to UniProtKB:  Q7Z6A9
PHAROS:  Q7Z6A9
GTEx:  ENSG00000186265 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z6A9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
UL144
E, F, G, H
118Macacine alphaherpesvirus 1Mutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
P [auth F],
R [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A],
L [auth C],
M [auth D],
N [auth D],
Q [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
K [auth A],
O [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.277 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.99α = 90
b = 77.2β = 91.67
c = 101.72γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
BUCCANEERmodel building
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Refinement description, Structure summary