6MOE | pdb_00006moe

Monomeric DARPin E2 complex with EpoR

• PDB DOI: https://doi.org/10.2210/pdb6MOE/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2018-10-04 Released: 2019-06-05 
• Deposition Author(s): Jude, K.M., Mohan, K., Garcia, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.230 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Topological control of cytokine receptor signaling induces differential effects in hematopoiesis.

Mohan, K., Ueda, G., Kim, A.R., Jude, K.M., Fallas, J.A., Guo, Y., Hafer, M., Miao, Y., Saxton, R.A., Piehler, J., Sankaran, V.G., Baker, D., Garcia, K.C.

(2019) Science 364

• PubMed: 31123111 
• DOI: https://doi.org/10.1126/science.aav7532
• Primary Citation Related Structures: 
  6MOE, 6MOF, 6MOG, 6MOH, 6MOI, 6MOJ, 6MOK, 6MOL


• PubMed Abstract: 
  

  Although tunable signaling by G protein-coupled receptors can be exploited through medicinal chemistry, a comparable pharmacological approach has been lacking for the modulation of signaling through dimeric receptors, such as those for cytokines. We present a strategy to modulate cytokine receptor signaling output by use of a series of designed C2-symmetric cytokine mimetics, based on the designed ankyrin repeat protein (DARPin) scaffold, that can systematically control erythropoietin receptor (EpoR) dimerization orientation and distance between monomers. We sampled a range of EpoR geometries by varying intermonomer angle and distance, corroborated by several ligand-EpoR complex crystal structures. Across the range, we observed full, partial, and biased agonism as well as stage-selective effects on hematopoiesis. This surrogate ligand strategy opens access to pharmacological modulation of therapeutically important cytokine and growth factor receptor systems.

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Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China.
Division of Biophysics, Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany.
Center for Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. [e-mail] [e-mail].
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. [e-mail] [e-mail].
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 87.41 kDa 
• Atom Count: 6,249 
• Modeled Residue Count: 755 
• Deposited Residue Count: 794 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E2 DARPin	A, B	168	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Erythropoietin receptor	C, D	229	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	I [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PO4	E [auth A], F [auth A], H [auth B], J [auth C], K [auth C], L [auth C], N [auth D], O [auth D], P [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	G [auth A], M [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.230 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/626

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.25	α = 90
b = 122.16	β = 90
c = 132.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-05 
Deposition Author(s): Jude, K.M., Mohan, K., Garcia, K.C.

Revision History  

• Version 1.0: 2019-06-05
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary