4YQX | pdb_00004yqx

Mouse IL-2 Bound to JES6-1 scFv Fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 
    0.204 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

Antibodies to Interleukin-2 Elicit Selective T Cell Subset Potentiation through Distinct Conformational Mechanisms.

Spangler, J.B.Tomala, J.Luca, V.C.Jude, K.M.Dong, S.Ring, A.M.Votavova, P.Pepper, M.Kovar, M.Garcia, K.C.

(2015) Immunity 42: 815-825

  • DOI: https://doi.org/10.1016/j.immuni.2015.04.015
  • Primary Citation Related Structures: 
    4YQX, 4YUE

  • PubMed Abstract: 

    Interleukin-2 (IL-2) is a pleiotropic cytokine that regulates immune cell homeostasis and has been used to treat a range of disorders including cancer and autoimmune disease. IL-2 signals via interleukin-2 receptor-β (IL-2Rβ):IL-2Rγ heterodimers on cells expressing high (regulatory T cells, Treg) or low (effector cells) amounts of IL-2Rα (CD25). When complexed with IL-2, certain anti-cytokine antibodies preferentially stimulate expansion of Treg (JES6-1) or effector (S4B6) cells, offering a strategy for targeted disease therapy. We found that JES6-1 sterically blocked the IL-2:IL-2Rβ and IL-2:IL-2Rγ interactions, but also allosterically lowered the IL-2:IL-2Rα affinity through a "triggered exchange" mechanism favoring IL-2Rα(hi) Treg cells, creating a positive feedback loop for IL-2Rα(hi) cell activation. Conversely, S4B6 sterically blocked the IL-2:IL-2Rα interaction, while also conformationally stabilizing the IL-2:IL-2Rβ interaction, thus stimulating all IL-2-responsive immune cells, particularly IL-2Rβ(hi) effector cells. These insights provide a molecular blueprint for engineering selectively potentiating therapeutic antibodies.


  • Organizational Affiliation
    • Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Macromolecule Content 

  • Total Structure Weight: 83.95 kDa 
  • Atom Count: 5,824 
  • Modeled Residue Count: 719 
  • Deposited Residue Count: 742 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
JES6-1 VH domainA [auth H],
D [auth N]
123Rattus norvegicusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
JES6-1 VL domainB [auth L],
E [auth O]
118Rattus norvegicusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-2C [auth A],
F [auth M]
130Mus musculusMutation(s): 0 
Gene Names: Il2Il-2
UniProt
Find proteins for P04351 (Mus musculus)
Explore P04351 
Go to UniProtKB:  P04351
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04351
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth B]4N-Glycosylation
Glycosylation Resources
GlyTouCan: G63564LA
GlyCosmos: G63564LA
GlyGen: G63564LA
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free:  0.204 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.024α = 90
b = 99.024β = 90
c = 198.7γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI108626

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Source and taxonomy
  • Version 1.2: 2017-07-26
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary