4NN5 | pdb_00004nn5

Cytokine receptor complex - Crystal form 1A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.201 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.170 (Depositor) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history

Literature

Structural basis of the proinflammatory signaling complex mediated by TSLP.

Verstraete, K.van Schie, L.Vyncke, L.Bloch, Y.Tavernier, J.Pauwels, E.Peelman, F.Savvides, S.N.

(2014) Nat Struct Mol Biol 21: 375-382

  • DOI: https://doi.org/10.1038/nsmb.2794
  • Primary Citation Related Structures: 
    4NN5, 4NN6, 4NN7

  • PubMed Abstract: 

    Thymic stromal lymphopoietin (TSLP), a cytokine produced by epithelial cells at barrier surfaces, is pivotal for the development of widespread chronic inflammatory disorders such as asthma and atopic dermatitis. The structure of the mouse TSLP-mediated signaling complex reveals how TSLP establishes extensive interfaces with its cognate receptor (TSLPR) and the shared interleukin 7 receptor α-chain (IL-7Rα) to evoke membrane-proximal receptor-receptor contacts poised for intracellular signaling. Binding of TSLP to TSLPR is a mechanistic prerequisite for recruitment of IL-7Rα to the high-affinity ternary complex, which we propose is coupled to a structural switch in TSLP at the crossroads of the cytokine-receptor interfaces. Functional interrogation of TSLP-receptor interfaces points to putative interaction hotspots that could be exploited for antagonist design. Finally, we derive the structural rationale for the functional duality of IL-7Rα and establish a consensus for the geometry of ternary complexes mediated by interleukin 2 (IL-2)-family cytokines.


  • Organizational Affiliation
    • Unit for Structural Biology, Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry & Microbiology, Ghent University, Ghent, Belgium.

Macromolecule Content 

  • Total Structure Weight: 63.63 kDa 
  • Atom Count: 4,152 
  • Modeled Residue Count: 489 
  • Deposited Residue Count: 565 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thymic stromal lymphopoietin130Mus musculusMutation(s): 1 
Gene Names: Tslp
UniProt & NIH Common Fund Data Resources
Find proteins for Q9JIE6 (Mus musculus)
Explore Q9JIE6 
Go to UniProtKB:  Q9JIE6
IMPC:  MGI:1855696
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JIE6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-7 receptor subunit alpha223Mus musculusMutation(s): 0 
Gene Names: Il7rIL7RA
UniProt
Find proteins for P16872 (Mus musculus)
Explore P16872 
Go to UniProtKB:  P16872
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16872
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytokine receptor-like factor 2212Mus musculusMutation(s): 1 
Gene Names: Crlf2CRLF2 (TSLPR)Crlm2Tpte2Tslpr
UniProt & NIH Common Fund Data Resources
Find proteins for Q8CII9 (Mus musculus)
Explore Q8CII9 
Go to UniProtKB:  Q8CII9
IMPC:  MGI:1889506
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8CII9
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q8CII9-1
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
E [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.201 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.170 (Depositor) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.06α = 90
b = 79.756β = 90
c = 52.138γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-02
    Changes: Database references
  • Version 1.2: 2014-04-16
    Changes: Database references
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-11-27
    Changes: Structure summary