5EH1

Crystal structure of the extracellular part of receptor 2 of human interferon gamma


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of human interferon-gamma receptor 2 reveals the structural basis for receptor specificity.

Mikulecky, P.Zahradnik, J.Kolenko, P.Cerny, J.Charnavets, T.Kolarova, L.Necasova, I.Pham, P.N.Schneider, B.

(2016) Acta Crystallogr D Struct Biol 72: 1017-1025

  • DOI: https://doi.org/10.1107/S2059798316012237
  • Primary Citation of Related Structures:  
    5EH1

  • PubMed Abstract: 

    Interferon-γ receptor 2 is a cell-surface receptor that is required for interferon-γ signalling and therefore plays a critical immunoregulatory role in innate and adaptive immunity against viral and also bacterial and protozoal infections. A crystal structure of the extracellular part of human interferon-γ receptor 2 (IFNγR2) was solved by molecular replacement at 1.8 Å resolution. Similar to other class 2 receptors, IFNγR2 has two fibronectin type III domains. The characteristic structural features of IFNγR2 are concentrated in its N-terminal domain: an extensive π-cation motif of stacked residues KWRWRH, a NAG-W-NAG sandwich (where NAG stands for N-acetyl-D-glucosamine) and finally a helix formed by residues 78-85, which is unique among class 2 receptors. Mass spectrometry and mutational analyses showed the importance of N-linked glycosylation to the stability of the protein and confirmed the presence of two disulfide bonds. Structure-based bioinformatic analysis revealed independent evolutionary behaviour of both receptor domains and, together with multiple sequence alignment, identified putative binding sites for interferon-γ and receptor 1, the ligands of IFNγR2.


  • Organizational Affiliation

    Institute of Biotechnology CAS, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon gamma receptor 2231Homo sapiensMutation(s): 0 
Gene Names: IFNGR2IFNGT1
UniProt & NIH Common Fund Data Resources
Find proteins for P38484 (Homo sapiens)
Explore P38484 
Go to UniProtKB:  P38484
PHAROS:  P38484
GTEx:  ENSG00000159128 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38484
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P38484-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CYS
Query on CYS

Download Ideal Coordinates CCD File 
B [auth A]CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.102α = 90
b = 58.102β = 90
c = 377.266γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
BALBESphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references
  • Version 1.2: 2018-04-18
    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: 2024-11-20
    Changes: Data collection, Database references, Structure summary