4Y5V

Diabody 305 complex with EpoR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
diabody 305 VH domain
A, D, G
130Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Diabody 305 VL domain
B, E, H
117Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Erythropoietin receptor
C, F, I
229Homo sapiensMutation(s): 2 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
P [auth D]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
Q [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]
K [auth B]
L [auth B]
M [auth B]
N [auth D]
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth D],
O [auth D],
R [auth E],
S [auth E],
T [auth E],
U [auth F],
V [auth G],
W [auth G],
X [auth H],
Y [auth H],
Z [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.73α = 90
b = 215.021β = 90
c = 171.905γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary