6NG3 | pdb_00006ng3

Crystal structure of human CD160 and HVEM complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 
    0.274 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.234 (Depositor) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6NG3

This is version 2.2 of the entry. See complete history

Literature

Structural Basis of CD160:HVEM Recognition.

Liu, W.Garrett, S.C.Fedorov, E.V.Ramagopal, U.A.Garforth, S.J.Bonanno, J.B.Almo, S.C.

(2019) Structure 27: 1286-1295.e4

  • DOI: https://doi.org/10.1016/j.str.2019.05.010
  • Primary Citation Related Structures: 
    6NG3, 6NG9, 6NGG

  • PubMed Abstract: 

    CD160 is a signaling molecule that interacts with herpes virus entry mediator (HVEM) and contributes to a wide range of immune responses, including T cell inhibition, natural killer cell activation, and mucosal immunity. GPI-anchored and transmembrane isoforms of CD160 share the same ectodomain responsible for HVEM engagement, which leads to bidirectional signaling. Despite the importance of the CD160:HVEM signaling axis and its therapeutic relevance, the structural and mechanistic basis underlying CD160-HVEM engagement has not been described. We report the crystal structures of the human CD160 extracellular domain and its complex with human HVEM. CD160 adopts a unique variation of the immunoglobulin fold and exists as a monomer in solution. The CD160:HVEM assembly exhibits a 1:1 stoichiometry and a binding interface similar to that observed in the BTLA:HVEM complex. Our work reveals the chemical and physical determinants underlying CD160:HVEM recognition and initiation of associated signaling processes.


  • Organizational Affiliation
    • Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.

Macromolecule Content 

  • Total Structure Weight: 27.51 kDa 
  • Atom Count: 1,616 
  • Modeled Residue Count: 203 
  • Deposited Residue Count: 250 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CD160 antigen,Tumor necrosis factor receptor superfamily member 14250Homo sapiensMutation(s): 0 
Gene Names: CD160BY55TNFRSF14HVEAHVEMUNQ329/PRO509
UniProt & NIH Common Fund Data Resources
Find proteins for O95971 (Homo sapiens)
Explore O95971 
Go to UniProtKB:  O95971
PHAROS:  O95971
GTEx:  ENSG00000117281 
Find proteins for Q92956 (Homo sapiens)
Explore Q92956 
Go to UniProtKB:  Q92956
PHAROS:  Q92956
GTEx:  ENSG00000157873 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO95971Q92956
Glycosylation
Glycosylation Sites: 2Go to GlyGen: O95971-1Q92956-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G31886NL
GlyCosmos: G31886NL
GlyGen: G31886NL
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free:  0.274 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.234 (Depositor) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.93α = 90
b = 87.93β = 90
c = 157.698γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesS10 OD020068

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary