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Open data
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Basic information
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Title | Chlorophyll-binding region of de novo-designed nanocage O32-15 | |||||||||
![]() | Chlorophyll-binding region of de novo-designed nanocage O32-15 | |||||||||
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![]() | nanocage / helical repeats / chlorophyll-binding / octahedral symmetry / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.2 Å | |||||||||
![]() | Redler RL / Ennist NM / Wang S / Baker D / Ekiert DC / 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 91.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.3 KB 19.3 KB | Display Display | ![]() |
Images | ![]() | 47 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() | 170.4 MB 170.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 763.3 KB | Display | ![]() |
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Full document | ![]() | 762.9 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | Chlorophyll-binding region of de novo-designed nanocage O32-15 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.076 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_40209_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_40209_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM
Entire | Name: Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM |
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Components |
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-Supramolecule #1: Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM
Supramolecule | Name: Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: C3-comp_O32-15
Macromolecule | Name: C3-comp_O32-15 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: STKEKARQLA EEAKETAEKV GDPELIKLAE QASQEGDSEK AKAILLAAEA ARVAKEVGAP DLIRLARIAA RVGASEAAKA ILLAAEAARV AKEVGDPELE RLALLAAVLG DSEKAKAILL AAEAARVAKE VGDPELIKLA LEAAERGDSE KAKAILLAAE AARVAKEVGD ...String: STKEKARQLA EEAKETAEKV GDPELIKLAE QASQEGDSEK AKAILLAAEA ARVAKEVGAP DLIRLARIAA RVGASEAAKA ILLAAEAARV AKEVGDPELE RLALLAAVLG DSEKAKAILL AAEAARVAKE VGDPELIKLA LEAAERGDSE KAKAILLAAE AARVAKEVGD PELIKLALEA ARRGDSEKAK AILLAAEAAR VAKEVGDPEL IKLALEAARR GDSRKAEAIL LAAEAARIAK EAGDPEARKK ALEAARRGDR ELATRILIEA LLRLLKKSTA ELKRATASLR AITEELKKNP SEDALVEHNR AIVEHNAIIV ENNRIIAMVL EAIVRAI |
-Macromolecule #2: C2-chlorophyll-comp_O32-15_ctermHis
Macromolecule | Name: C2-chlorophyll-comp_O32-15_ctermHis / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: DEEFKFLATE AKMLITAAER LAGTDPRLQE MVALIKKELE QAERTFRNGD KSEAQRQLEF VLTAARAVMN VAAAANAAGT DPLLKAMVDA ILWRLKEAIR TFQNGDQEEA ETQLRFVLRA AIAVAVVAAA LVLAGTDPEL QEMVEQIKDL LISAFMAGAR GDKEKALTQL ...String: DEEFKFLATE AKMLITAAER LAGTDPRLQE MVALIKKELE QAERTFRNGD KSEAQRQLEF VLTAARAVMN VAAAANAAGT DPLLKAMVDA ILWRLKEAIR TFQNGDQEEA ETQLRFVLRA AIAVAVVAAA LVLAGTDPEL QEMVEQIKDL LISAFMAGAR GDKEKALTQL LFVAWAAHAV AMIAAAANLA GTDPRLQQQV KEILEKLKEA IETFQKGDEE QAFRQLAEVL AEAALVALRA ALTNLEHHHH HH |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Average exposure time: 2.0 sec. / Average electron dose: 49.99 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |