6MOG | pdb_00006mog

Dimeric DARPin C_R3

• PDB DOI: https://doi.org/10.2210/pdb6MOG/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-04 Released: 2019-06-05 
• Deposition Author(s): Jude, K.M., Mohan, K., Garcia, K.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: in silico

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 35.9 kDa 
• Atom Count: 2,641 
• Modeled Residue Count: 315 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin C_R3	A, B	165	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	M [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/624

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.25	α = 90
b = 89.81	β = 99.13
c = 44.27	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI51321

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: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description