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- PDB-8glt: Backbone model of de novo-designed chlorophyll-binding nanocage O32-15 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8glt | |||||||||
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Title | Backbone model of de novo-designed chlorophyll-binding nanocage O32-15 | |||||||||
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![]() | DE NOVO PROTEIN / nanocage / helical repeats / chlorophyll-binding / octahedral symmetry | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
![]() | Redler, R.L. / Ennist, N.M. / Wang, S. / Baker, D. / Ekiert, D.C. / Bhabha, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: De novo design of proteins housing excitonically coupled chlorophyll special pairs. Authors: Nathan M Ennist / Shunzhi Wang / Madison A Kennedy / Mariano Curti / George A Sutherland / Cvetelin Vasilev / Rachel L Redler / Valentin Maffeis / Saeed Shareef / Anthony V Sica / Ash Sueh ...Authors: Nathan M Ennist / Shunzhi Wang / Madison A Kennedy / Mariano Curti / George A Sutherland / Cvetelin Vasilev / Rachel L Redler / Valentin Maffeis / Saeed Shareef / Anthony V Sica / Ash Sueh Hua / Arundhati P Deshmukh / Adam P Moyer / Derrick R Hicks / Avi Z Swartz / Ralph A Cacho / Nathan Novy / Asim K Bera / Alex Kang / Banumathi Sankaran / Matthew P Johnson / Amala Phadkule / Mike Reppert / Damian Ekiert / Gira Bhabha / Lance Stewart / Justin R Caram / Barry L Stoddard / Elisabet Romero / C Neil Hunter / David Baker / ![]() ![]() ![]() 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 ...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-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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.9 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 40208MC ![]() 7unhC ![]() 7uniC ![]() 7unjC ![]() 8evmC M: map data used to model this data C: citing same article ( |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 35889.559 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Protein | Mass: 27799.957 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: synthetic construct (others) |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 300 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 49.99 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 |
EM imaging optics | Energyfilter slit width: 20 eV |
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Processing
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EM software |
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CTF correction | Details: Patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 359331 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: O (octahedral) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205014 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 0 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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