8ENT

Interleukin-21 signaling complex with IL-21R and IL-2Rg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A structural blueprint for interleukin-21 signal modulation.

Abhiraman, G.C.Bruun, T.U.J.Caveney, N.A.Su, L.L.Saxton, R.A.Yin, Q.Tang, S.Davis, M.M.Jude, K.M.Garcia, K.C.

(2023) Cell Rep 42: 112657-112657

  • DOI: https://doi.org/10.1016/j.celrep.2023.112657
  • Primary Citation of Related Structures:  
    8ENT

  • PubMed Abstract: 

    Interleukin-21 (IL-21) plays a critical role in generating immunological memory by promoting the germinal center reaction, yet clinical use of IL-21 remains challenging because of its pleiotropy and association with autoimmune disease. To better understand the structural basis of IL-21 signaling, we determine the structure of the IL-21-IL-21R-γc ternary signaling complex by X-ray crystallography and a structure of a dimer of trimeric complexes using cryo-electron microscopy. Guided by the structure, we design analogs of IL-21 by introducing substitutions to the IL-21-γc interface. These IL-21 analogs act as partial agonists that modulate downstream activation of pS6, pSTAT3, and pSTAT1. These analogs exhibit differential activity on T and B cell subsets and modulate antibody production in human tonsil organoids. These results clarify the structural basis of IL-21 signaling and offer a potential strategy for tunable manipulation of humoral immunity.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-21
A, D, G, J
144Homo sapiensMutation(s): 1 
Gene Names: IL21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBE4 (Homo sapiens)
Explore Q9HBE4 
Go to UniProtKB:  Q9HBE4
PHAROS:  Q9HBE4
GTEx:  ENSG00000138684 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HBE4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-21 receptor
B, E, H, K
237Homo sapiensMutation(s): 4 
Gene Names: IL21RNILRUNQ3121/PRO10273
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBE5 (Homo sapiens)
Explore Q9HBE5 
Go to UniProtKB:  Q9HBE5
PHAROS:  Q9HBE5
GTEx:  ENSG00000103522 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HBE5
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9HBE5-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytokine receptor common subunit gamma
C, F, I
207Homo sapiensMutation(s): 1 
Gene Names: IL2RG
UniProt & NIH Common Fund Data Resources
Find proteins for P31785 (Homo sapiens)
Explore P31785 
Go to UniProtKB:  P31785
PHAROS:  P31785
GTEx:  ENSG00000147168 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31785
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P31785-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
L, M, O
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth I]
BA [auth I]
P [auth C]
R [auth C]
U [auth E]
AA [auth I],
BA [auth I],
P [auth C],
R [auth C],
U [auth E],
X [auth F],
Z [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth I]
DA [auth I]
EA [auth K]
FA [auth K]
GA [auth K]
CA [auth I],
DA [auth I],
EA [auth K],
FA [auth K],
GA [auth K],
HA [auth K],
IA [auth K],
JA [auth K],
Q [auth C],
S [auth C],
T [auth D],
V [auth E],
W [auth E],
Y [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.167α = 83.34
b = 66.464β = 83.71
c = 162.684γ = 73.1
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
XDSdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesRO1-AI51321
Bill & Melinda Gates FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary