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Yorodumi- EMDB-40208: Backbone model of de novo-designed chlorophyll-binding nanocage O32-15 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40208 | |||||||||
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Title | Backbone model of de novo-designed chlorophyll-binding nanocage O32-15 | |||||||||
Map data | Backbone model of de novo-designed chlorophyll-binding nanocage O32-15 | |||||||||
Sample |
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Keywords | nanocage / helical repeats / chlorophyll-binding / octahedral symmetry / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Redler RL / Ennist NM / Wang S / Baker D / Ekiert DC / Bhabha G | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Chem Biol / Year: 2024 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 | emd_40208.map.gz | 86.8 MB | EMDB map data format | |
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Header (meta data) | emd-40208-v30.xml emd-40208.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
Images | emd_40208.png | 57.3 KB | ||
Filedesc metadata | emd-40208.cif.gz | 6.1 KB | ||
Others | emd_40208_half_map_1.map.gz emd_40208_half_map_2.map.gz | 170.3 MB 170.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40208 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40208 | HTTPS FTP |
-Related structure data
Related structure data | 8gltMC 7unhC 7uniC 7unjC 8evmC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40208.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Backbone model of de novo-designed chlorophyll-binding nanocage O32-15 | ||||||||||||||||||||
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_40208_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_40208_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-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, polyalanine model
Macromolecule | Name: C3-comp_O32-15, polyalanine model / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 35.889559 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSTKEKARQL AEEAKETAEK VGDPELIKLA EQASQEGDSE KAKAILLAAE AARVAKEVGA PDLIRLARIA ARVGASEAAK AILLAAEAA RVAKEVGDPE LERLALLAAV LGDSEKAKAI LLAAEAARVA KEVGDPELIK LALEAAERGD SEKAKAILLA A EAARVAKE ...String: MSTKEKARQL AEEAKETAEK VGDPELIKLA EQASQEGDSE KAKAILLAAE AARVAKEVGA PDLIRLARIA ARVGASEAAK AILLAAEAA RVAKEVGDPE LERLALLAAV LGDSEKAKAI LLAAEAARVA KEVGDPELIK LALEAAERGD SEKAKAILLA A EAARVAKE VGDPELIKLA LEAARRGDSE KAKAILLAAE AARVAKEVGD PELIKLALEA ARRGDSRKAE AILLAAEAAR IA KEAGDPE ARKKALEAAR RGDRELATRI LIEALLRLLK KSTAELKRAT ASLRAITEEL KKNPSEDALV EHNRAIVEHN AII VENNRI IAMVLEAIVR AI |
-Macromolecule #2: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
Macromolecule | Name: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 27.799957 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDEEFKFLAT EAKMLITAAE RLAGTDPRLQ EMVALIKKEL EQAERTFRNG DKSEAQRQLE FVLTAARAVM NVAAAANAAG TDPLLKAMV DAILWRLKEA IRTFQNGDQE EAETQLRFVL RAAIAVAVVA AALVLAGTDP ELQEMVEQIK DLLISAFMAG A RGDKEKAL ...String: MDEEFKFLAT EAKMLITAAE RLAGTDPRLQ EMVALIKKEL EQAERTFRNG DKSEAQRQLE FVLTAARAVM NVAAAANAAG TDPLLKAMV DAILWRLKEA IRTFQNGDQE EAETQLRFVL RAAIAVAVVA AALVLAGTDP ELQEMVEQIK DLLISAFMAG A RGDKEKAL TQLLFVAWAA HAVAMIAAAA NLAGTDPRLQ QQVKEILEKL KEAIETFQKG DEEQAFRQLA EVLAEAALVA LR AALTNLE HHHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: FIELD EMISSION GUN |
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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8glt: |