8GLT | pdb_00008glt

Backbone model of de novo-designed chlorophyll-binding nanocage O32-15

• PDB DOI: https://doi.org/10.2210/pdb8GLT/pdb
• EM Map EMD-40208: EMDB EMDataResource

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


• Deposited: 2023-03-23 Released: 2024-03-27 
• Deposition Author(s): Redler, R.L., Ennist, N.M., Wang, S., Baker, D., Ekiert, D.C., Bhabha, G.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA), Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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 20: 906-915

• PubMed: 38831036 
• DOI: https://doi.org/10.1038/s41589-024-01626-0
• Primary Citation 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.

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Organizational Affiliation: 
• Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain.
School of Biosciences, University of Sheffield, Sheffield, UK.
Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.
Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain.
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Department of Chemistry, Purdue University, West Lafayette, IN, USA.
Department of Microbiology, New York University School of Medicine, New York, NY, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Hetero 48-mer - A24B24 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,528.55 kDa 
• Atom Count: 67,992 
• Modeled Residue Count: 13,704 
• Deposited Residue Count: 14,184 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C3-comp_O32-15, polyalanine model	A [auth 0], AA [auth 4], BA [auth 6], CA [auth 8], DA [auth A], EA [auth AB], FA [auth AC], GA [auth AE], HA [auth AF], IA [auth AG], JA [auth AH], KA [auth C], LA [auth E], MA [auth G], NA [auth I], OA [auth K], PA [auth M], QA [auth O], RA [auth Q], SA [auth S], TA [auth U], UA [auth W], VA [auth Y], Z [auth 2]	338	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model	B [auth 1], C [auth 3], D [auth 5], E [auth 7], F [auth 9], G [auth B], H [auth BA], I [auth BB], J [auth BC], K [auth BD], L [auth BE], M [auth BF], N [auth D], O [auth F], P [auth H], Q [auth J], R [auth L], S [auth N], T [auth P], U [auth R], V [auth T], W [auth V], X, Y [auth Z]	253	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.0
MODEL REFINEMENT	PHENIX	1.16
MODEL REFINEMENT	Coot	0.8.9.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Redler, R.L., Ennist, N.M., Wang, S., Baker, D., Ekiert, D.C., Bhabha, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	5U19AG065156-02
Other private		--

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release
  
• Version 1.1: 2024-06-12
  Changes: Database references
• Version 1.2: 2024-07-10
  Changes: Data collection, Database references