7UNH

De novo designed chlorophyll dimer protein in apo state, SP2

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

  • Deposited: 2022-04-11 Released: 2023-04-19 
  • Deposition Author(s): Kennedy, M.A., Stoddard, B.L., Ennist, N.M.
  • Funding Organization(s): National Science Foundation (NSF, United States), Advanced Research Projects Agency-Energy (ARPA-E), Audacious Project at the Institute for Protein Design, National Institutes of Health/Office of the Director

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.214 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

De novo design of proteins housing excitonically coupled chlorophyll special pairs.

Ennist, N.M.Wang, S.Kennedy, M.A.Curti, M.Sutherland, G.A.Vasilev, C.Redler, R.L.Maffeis, V.Shareef, S.Sica, A.V.Hua, A.S.Deshmukh, A.P.Moyer, A.P.Hicks, D.R.Swartz, A.Z.Cacho, R.A.Novy, N.Bera, A.K.Kang, A.Sankaran, B.Johnson, M.P.Phadkule, A.Reppert, M.Ekiert, D.Bhabha, G.Stewart, L.Caram, J.R.Stoddard, B.L.Romero, E.Hunter, C.N.Baker, D.

(2024) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-024-01626-0
  • Primary Citation of Related Structures:  
    7UNH, 7UNI, 7UNJ, 8EVM, 8GLT

  • PubMed Abstract: 

    Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C 2 -symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.


  • Organizational Affiliation

    Institute for Protein Design, University of Washington, Seattle, WA, USA. ennist@uw.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SP2 designed chlorophyll dimer protein
A, B
246synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.131α = 90
b = 76.14β = 99.06
c = 63.234γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
CrysalisProdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDGE-1762114
Advanced Research Projects Agency-Energy (ARPA-E)DE-AR0001543
Audacious Project at the Institute for Protein Design68-2492: Audacious GC5: Next-Generation Nanoengineering
National Institutes of Health/Office of the DirectorUnited States1S10OD028581-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-06-12
    Changes: Database references