4Y5X

Diabody 305 complex with EpoR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


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 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 310 VL domain
A, D, G, J
136Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
diabody 310 VH domain
B, E, H, K
116Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q5NV67 (Homo sapiens)
Explore Q5NV67 
Go to UniProtKB:  Q5NV67
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5NV67
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Erythropoietin receptor
C, F, I, L
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
AA [auth K]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth L]
CA [auth L]
DA [auth L]
M [auth A]
N [auth B]
BA [auth L],
CA [auth L],
DA [auth L],
M [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth E],
U [auth F],
V [auth G],
W [auth G],
X [auth H],
Y [auth J],
Z [auth K]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 239.54α = 90
b = 239.54β = 90
c = 132.569γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
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: 2017-11-22
    Changes: Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary