+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28889 | |||||||||
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Title | CryoEM structure of designed modular protein oligomer C6-79 | |||||||||
Map data | CryoEM structure of designed modular protein oligomer C6-79 | |||||||||
Sample |
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Keywords | Synthetic / Self-assembling / Oligomeric / Helical repeats / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Redler RL / Edman NI / Baker D / Ekiert D / Bhabha G | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: FGF receptor activation using designed cyclic oligomeric assemblies Authors: Redler RL / Edman NI / Baker D / Ekiert D / Bhabha G | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28889.map.gz | 38.1 MB | EMDB map data format | |
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Header (meta data) | emd-28889-v30.xml emd-28889.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
Images | emd_28889.png | 110.7 KB | ||
Filedesc metadata | emd-28889.cif.gz | 5.5 KB | ||
Others | emd_28889_half_map_1.map.gz emd_28889_half_map_2.map.gz | 37.6 MB 37.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28889 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28889 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28889.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | CryoEM structure of designed modular protein oligomer C6-79 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.069 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_28889_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_28889_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Self-assembled homo-hexamer of de novo designed protein C6-79
Entire | Name: Self-assembled homo-hexamer of de novo designed protein C6-79 |
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Components |
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-Supramolecule #1: Self-assembled homo-hexamer of de novo designed protein C6-79
Supramolecule | Name: Self-assembled homo-hexamer of de novo designed protein C6-79 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: De novo designed oligomeric protein C6-79
Macromolecule | Name: De novo designed oligomeric protein C6-79 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 26.884201 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MGSSDEEEAR ELEERAREAA KRAIEAAKRT GDPRVRELAE ELVKLAIWAA VEVWLDPSSS DVNEALKLIV EAIEAAVRAL EAAERTGDP EVRELARELV RLAVEAAEEV QRNPSSSDVN EALKLIVIAI EAAVRALEAA ERTGDPEVRE LARELVRLAV E AAEEVQRN ...String: MGSSDEEEAR ELEERAREAA KRAIEAAKRT GDPRVRELAE ELVKLAIWAA VEVWLDPSSS DVNEALKLIV EAIEAAVRAL EAAERTGDP EVRELARELV RLAVEAAEEV QRNPSSSDVN EALKLIVIAI EAAVRALEAA ERTGDPEVRE LARELVRLAV E AAEEVQRN PSSEEVNEAL RKIIKLILFA VMVLELAEEI GDPTWREMAR RAVREAVELA EEVQRDPSGW LGHGSLEHHH HH H |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: blot time = 6s; blot force = 0. |
-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: 0.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6434 / Average exposure time: 2.5 sec. / Average electron dose: 61.3 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE / Details: Ab initio model generated in Cryosparc |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 864566 |
-Atomic model buiding 1
Details | Designed oligomer was used as initial model and was initially fit into map using UCSF Chimera |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: Correlation coefficients |
Output model | PDB-8f6r: |