+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28888 | |||||||||
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Title | CryoEM structure of designed modular protein oligomer C8-71 | |||||||||
Map data | CryoEM structure of designed modular protein oligomer C8-71 | |||||||||
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: 3.6 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_28888.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-28888-v30.xml emd-28888.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
Images | emd_28888.png | 126.2 KB | ||
Filedesc metadata | emd-28888.cif.gz | 5.7 KB | ||
Others | emd_28888_half_map_1.map.gz emd_28888_half_map_2.map.gz | 28.2 MB 28.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28888 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28888 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28888.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | CryoEM structure of designed modular protein oligomer C8-71 | ||||||||||||||||||||
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_28888_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_28888_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-octamer of de novo designed protein C8-71
Entire | Name: Self-assembled homo-octamer of de novo designed protein C8-71 |
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Components |
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-Supramolecule #1: Self-assembled homo-octamer of de novo designed protein C8-71
Supramolecule | Name: Self-assembled homo-octamer of de novo designed protein C8-71 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: C8-71
Macromolecule | Name: C8-71 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 23.435004 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MGPEEILERA KESLERAREA SERGDEEEFR KAAEKALELA KRLVEQAKKE GDPELVLEAA RVALWVAELA AKNGDKEVFK KAAESALEV AKRLVEVASK EGDPDLVAWA ALVALWVAFL AFLNGDKEVF KKAAESALEV AKALMEVAMK VGAPWLVELA I AVARAVWL ...String: MGPEEILERA KESLERAREA SERGDEEEFR KAAEKALELA KRLVEQAKKE GDPELVLEAA RVALWVAELA AKNGDKEVFK KAAESALEV AKRLVEVASK EGDPDLVAWA ALVALWVAFL AFLNGDKEVF KKAAESALEV AKALMEVAMK VGAPWLVELA I AVARAVWL LAELFGDEEV RRRAEAFEII LRIAAIAVKA WLGGGGSLEH HHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation #1
Preparation ID | 1 |
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Concentration | 0.9 mg/mL |
Buffer | pH: 8 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY ARRAY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - 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 / Details: blot time = 4s; blot force = 0. |
Details | Sample present within the ice layer as both isolated homo-octameric rings and fibrils of variable length |
-Sample preparation #2
Preparation ID | 2 |
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Concentration | 0.9 mg/mL |
Buffer | pH: 8 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY ARRAY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - 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 / Details: blot time = 4s; blot force = 0. |
Details | Sample present within the ice layer as both isolated homo-octameric rings and fibrils of variable length |
-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: 2 / Number real images: 3092 / 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: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 132391 |
-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-8f6q: |