+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40209 | |||||||||
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Title | Chlorophyll-binding region of de novo-designed nanocage O32-15 | |||||||||
Map data | Chlorophyll-binding region of de novo-designed 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: 5.2 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: To Be Published Title: De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs Authors: Ennist NM / Wang S / Kennedy MA / Curti M / Sutherland GA / Vasilev C / Redler RL / Maffeis V / Shareef S / Sica AV / Hua AS / Deshmukh AP / Moyer AP / Hicks DR / Swartz AZ / Cacho RA / Novy ...Authors: Ennist NM / Wang S / Kennedy MA / Curti M / Sutherland GA / Vasilev C / Redler RL / Maffeis V / Shareef S / Sica AV / Hua AS / Deshmukh AP / Moyer AP / Hicks DR / Swartz AZ / Cacho RA / Novy N / Bera AK / Kang A / Sankaran B / Johnson MP / Reppert M / Ekiert DC / Bhabha G / Stewart L / Caram JR / Stoddard BL / Romero E / Hunter CN / Baker D | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40209.map.gz | 91.8 MB | EMDB map data format | |
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Header (meta data) | emd-40209-v30.xml emd-40209.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_40209.png | 47 KB | ||
Filedesc metadata | emd-40209.cif.gz | 5.7 KB | ||
Others | emd_40209_half_map_1.map.gz emd_40209_half_map_2.map.gz | 170.4 MB 170.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40209 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40209 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40209.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Chlorophyll-binding region of de novo-designed 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_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 |
-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: Escherichia coli (E. coli) |
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: Escherichia coli (E. coli) |
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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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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 64000 |
Specialist optics | Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 359331 |
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Startup model | Type of model: NONE |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) Details: Particles were symmetry-expanded and partial-signal-subtracted prior to final refinement (Local Refinement in Cryosparc). Resolution of 5.2A is median resolution from Local Resolution Estimation in Cryosparc. Number images used: 2844504 |