6OEL

Engineered Fab bound to IL-4 receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report



Literature

A strategy for the selection of monovalent antibodies that span protein dimer interfaces.

Spangler, J.B.Moraga, I.Jude, K.M.Savvides, C.S.Garcia, K.C.

(2019) J Biol Chem 294: 13876-13886

  • DOI: 10.1074/jbc.RA119.009213
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ligand-induced dimerization is the predominant mechanism through which secreted proteins activate cell surface receptors to transmit essential biological signals. Cytokines are a large class of soluble proteins that dimerize transmembrane receptors into precise signaling topologies, but there is a need for alternative, engineerable ligand scaffolds that specifically recognize and stabilize these protein interactions ...

    Ligand-induced dimerization is the predominant mechanism through which secreted proteins activate cell surface receptors to transmit essential biological signals. Cytokines are a large class of soluble proteins that dimerize transmembrane receptors into precise signaling topologies, but there is a need for alternative, engineerable ligand scaffolds that specifically recognize and stabilize these protein interactions. Recombinant antibodies can potentially serve as robust and versatile platforms for cytokine complex stabilization, and their specificity allows for tunable modulation of dimerization equilibrium. Here, we devised an evolutionary strategy to isolate monovalent antibody fragments that bridge together two different receptor subunits in a cytokine-receptor complex, precisely as the receptors are disposed in their natural signaling orientations. To do this, we screened a naive antibody library against a stabilized ligand-receptor ternary complex that acted as a "molecular cast" of the natural receptor dimer conformation. Our selections elicited "stapler" single-chain variable fragments (scFvs) of antibodies that specifically engage the interleukin-4 receptor heterodimer. The 3.1 Å resolution crystal structure of one such stapler revealed that, as intended, this scFv recognizes a composite epitope between the two receptors as they are positioned in the complex. Extending our approach, we evolved a stapler scFv that specifically binds to and stabilizes the interface between the interleukin-2 cytokine and one of its receptor subunits, leading to a 15-fold enhancement in interaction affinity. This demonstration that scFvs can be selected to recognize epitopes that span protein interfaces presents new opportunities to engineer structurally defined antibodies for a broad range of research and therapeutic applications.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
engineered Interleukin-4, RGA variantA129Homo sapiensMutation(s): 8 
Gene Names: IL4
Find proteins for P05112 (Homo sapiens)
Explore P05112 
Go to UniProtKB:  P05112
NIH Common Fund Data Resources
PHAROS  P05112
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-4 receptor subunit alphaB202Homo sapiensMutation(s): 0 
Gene Names: IL4RIL4RA582J2.1
Find proteins for P24394 (Homo sapiens)
Explore P24394 
Go to UniProtKB:  P24394
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PHAROS  P24394
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytokine receptor common subunit gammaC189Homo sapiensMutation(s): 1 
Gene Names: IL2RG
Find proteins for P31785 (Homo sapiens)
Explore P31785 
Go to UniProtKB:  P31785
NIH Common Fund Data Resources
PHAROS  P31785
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
engineered Fab heavy chainH229Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
engineered Fab light chainL224Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
B, C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NO3
Query on NO3

Download CCD File 
H
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: F 41 3 2
  • Diffraction Data DOI: 10.15785/SBGRID/652 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 328.1α = 90
b = 328.1β = 90
c = 328.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata 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 AI51321

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-02
    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: Atomic model, Data collection, Derived calculations, Structure summary