4Y5Y | pdb_00004y5y

Diabody 330 complex with EpoR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.241 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.226 (DCC) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4Y5Y

This is version 1.3 of the entry. See complete history

Literature

Tuning Cytokine Receptor Signaling by Re-orienting Dimer Geometry with Surrogate Ligands.

Moraga, I.Wernig, G.Wilmes, S.Gryshkova, V.Richter, C.P.Hong, W.J.Sinha, R.Guo, F.Fabionar, H.Wehrman, T.S.Krutzik, P.Demharter, S.Plo, I.Weissman, I.L.Minary, P.Majeti, R.Constantinescu, S.N.Piehler, J.Garcia, K.C.

(2015) Cell 160: 1196-1208

  • DOI: https://doi.org/10.1016/j.cell.2015.02.011
  • Primary Citation Related Structures: 
    4Y5V, 4Y5X, 4Y5Y

  • PubMed Abstract: 

    Most cell-surface receptors for cytokines and growth factors signal as dimers, but it is unclear whether remodeling receptor dimer topology is a viable strategy to "tune" signaling output. We utilized diabodies (DA) as surrogate ligands in a prototypical dimeric receptor-ligand system, the cytokine Erythropoietin (EPO) and its receptor (EpoR), to dimerize EpoR ectodomains in non-native architectures. Diabody-induced signaling amplitudes varied from full to minimal agonism, and structures of these DA/EpoR complexes differed in EpoR dimer orientation and proximity. Diabodies also elicited biased or differential activation of signaling pathways and gene expression profiles compared to EPO. Non-signaling diabodies inhibited proliferation of erythroid precursors from patients with a myeloproliferative neoplasm due to a constitutively active JAK2V617F mutation. Thus, intracellular oncogenic mutations causing ligand-independent receptor activation can be counteracted by extracellular ligands that re-orient receptors into inactive dimer topologies. This approach has broad applications for tuning signaling output for many dimeric receptor systems.


  • Organizational Affiliation
    • Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5345, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305-5345, USA.

Macromolecule Content 

  • Total Structure Weight: 102.43 kDa 
  • Atom Count: 6,531 
  • Modeled Residue Count: 868 
  • Deposited Residue Count: 952 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
diabody 330 VH domain
A, D
130Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
diabody 330 VL domain
B, E
117Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Erythropoietin receptor
C, F
229Homo sapiensMutation(s): 4 
Gene Names: EPOR
UniProt & NIH Common Fund Data Resources
Find proteins for P19235 (Homo sapiens)
Explore P19235 
Go to UniProtKB:  P19235
PHAROS:  P19235
GTEx:  ENSG00000187266 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19235
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, D
L-PEPTIDE LINKINGC8 H18 N2 O2LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.241 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.226 (DCC) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.141α = 90
b = 95.799β = 90
c = 144.972γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description