8F6R

CryoEM structure of designed modular protein oligomer C6-79


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.

Edman, N.I.Phal, A.Redler, R.L.Schlichthaerle, T.Srivatsan, S.R.Ehnes, D.D.Etemadi, A.An, S.J.Favor, A.Li, Z.Praetorius, F.Gordon, M.Vincent, T.Marchiano, S.Blakely, L.Lin, C.Yang, W.Coventry, B.Hicks, D.R.Cao, L.Bethel, N.Heine, P.Murray, A.Gerben, S.Carter, L.Miranda, M.Negahdari, B.Lee, S.Trapnell, C.Zheng, Y.Murry, C.E.Schweppe, D.K.Freedman, B.S.Stewart, L.Ekiert, D.C.Schlessinger, J.Shendure, J.Bhabha, G.Ruohola-Baker, H.Baker, D.

(2024) Cell 187: 3726-3740.e43

  • DOI: https://doi.org/10.1016/j.cell.2024.05.025
  • Primary Citation of Related Structures:  
    8F6R

  • PubMed Abstract: 

    Many growth factors and cytokines signal by binding to the extracellular domains of their receptors and driving association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affect signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo-designed fibroblast growth factor receptor (FGFR)-binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca 2+ release and mitogen-activated protein kinase (MAPK) pathway activation. The high specificity of the designed agonists reveals distinct roles for two FGFR splice variants in driving arterial endothelium and perivascular cell fates during early vascular development. Our designed modular assemblies should be broadly useful for unraveling the complexities of signaling in key developmental transitions and for developing future therapeutic applications.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
De novo designed oligomeric protein C6-79
A, B, C, D, E
A, B, C, D, E, F
241synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM128777
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR01AG063845

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Database references
  • Version 1.3: 2024-06-26
    Changes: Data collection, Database references
  • Version 1.4: 2024-07-24
    Changes: Data collection, Database references