9E2T | pdb_00009e2t

Structure of a de novo designed interleukin-21 mimetic complex with IL-21R and IL-2Rg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design of a potent interleukin-21 mimic for cancer immunotherapy.

Chun, J.H.Lim, B.S.Roy, S.Walsh, M.J.Abhiraman, G.C.Zhangxu, K.Atajanova, T.Revach, O.Y.Clark, E.C.Li, P.Palin, C.A.Khanna, A.Tower, S.Kureshi, R.Hoffman, M.T.Sharova, T.Lawless, A.Cohen, S.Boland, G.M.Nguyen, T.Peprah, F.Tello, J.G.Liu, S.Y.Kim, C.J.Shin, H.Quijano-Rubio, A.Jude, K.M.Gerben, S.Murray, A.Heine, P.DeWitt, M.Ulge, U.Y.Carter, L.King, N.P.Silva, D.A.Kueh, H.Y.Kalia, V.Sarkar, S.Jenkins, R.W.Garcia, K.C.Leonard, W.J.Dougan, M.Dougan, S.K.Baker, D.

(2025) Sci Immunol 10: eadx1582-eadx1582

  • DOI: https://doi.org/10.1126/sciimmunol.adx1582
  • Primary Citation of Related Structures:  
    9E2T

  • PubMed Abstract: 

    Long-standing goals of cancer immunotherapy are to activate cytotoxic antitumor T cells across a range of affinities for tumor antigens while suppressing regulatory T cells. Computational protein design has enabled the precise tailoring of proteins to meet specific needs. Here, we report a de novo designed IL-21 mimic, 21h10, with high stability and signaling potency in humans and mice. In murine and ex vivo human organotypic tumor models, 21h10 showed robust antitumor activity, with more prolonged signaling and stronger antitumor activity than native IL-21. 21h10 induced pancreatitis that could be mitigated by TNF blockade without compromising antitumor efficacy. Although antidrug antibodies to 21h10 formed, they were not neutralizing. 21h10 induced highly cytotoxic T cells with a range of affinities, robustly expanding intratumoral low-affinity cytotoxic T cells and driving high expression of IFN-γ and granzyme B compared with native IL-21, while increasing the frequency of IFN-γ + T helper 1 cells and reducing regulatory T cells. The full human-mouse cross-reactivity, high stability and potency, and low-affinity antitumor responses support the translational potential of 21h10.


  • Organizational Affiliation
    • Institute for Protein Design, University of Washington, Seattle, WA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
21h10
A, D, G, I
102synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-21 receptor
B, E, H, J
212Homo 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
203Homo sapiensMutation(s): 0 
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: 2Go to GlyGen: P31785-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth B]
N [auth C]
O [auth C]
P [auth C]
T [auth E]
K [auth B],
N [auth C],
O [auth C],
P [auth C],
T [auth E],
V [auth F],
W [auth F],
X [auth H],
Z [auth J]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth J]
L [auth B]
M [auth B]
Q [auth C]
AA [auth J],
BA [auth J],
L [auth B],
M [auth B],
Q [auth C],
R [auth C],
S [auth C],
U [auth E],
Y [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.499α = 94.63
b = 78.082β = 103.39
c = 101.219γ = 114.55
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release
  • Version 1.1: 2025-10-08
    Changes: Database references