+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: bioRxiv / Year: 2023 Title: Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Authors: Natasha I Edman / Rachel L Redler / Ashish Phal / Thomas Schlichthaerle / Sanjay R Srivatsan / Ali Etemadi / Seong J An / Andrew Favor / Devon Ehnes / Zhe Li / Florian Praetorius / Max ...Authors: Natasha I Edman / Rachel L Redler / Ashish Phal / Thomas Schlichthaerle / Sanjay R Srivatsan / Ali Etemadi / Seong J An / Andrew Favor / Devon Ehnes / Zhe Li / Florian Praetorius / Max Gordon / Wei Yang / Brian Coventry / Derrick R Hicks / Longxing Cao / Neville Bethel / Piper Heine / Analisa Murray / Stacey Gerben / Lauren Carter / Marcos Miranda / Babak Negahdari / Sangwon Lee / Cole Trapnell / Lance Stewart / Damian C Ekiert / Joseph Schlessinger / Jay Shendure / Gira Bhabha / Hannele Ruohola-Baker / David Baker / Abstract: Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, ...Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways. #2: Journal: Cell(Cambridge,Mass.) / Year: 2024 Title: Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies Authors: Edman NI / Redler RL / Phal A / Schlichthaerle T / Srivatsan SR / Etemadi A / An SJ / Favor A / Ehnes D / Li Z / Praetorius F / Gordon M / Yang W / Coventry B / Hicks DR / Cao L / Bethel N / ...Authors: Edman NI / Redler RL / Phal A / Schlichthaerle T / Srivatsan SR / Etemadi A / An SJ / Favor A / Ehnes D / Li Z / Praetorius F / Gordon M / Yang W / Coventry B / Hicks DR / Cao L / Bethel N / Heine P / Murray A / Gerben S / Carter L / Miranda M / Negahdari B / Lee S / Trapnell C / Stewart L / Ekiert DC / Schlessinger J / Shendure J / Bhabha G / Ruohola-Baker H / Baker D | |||||||||
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 | 25.3 KB 25.3 KB | Display Display | EMDB header |
Images | emd_28888.png | 126.2 KB | ||
Filedesc metadata | emd-28888.cif.gz | 6.6 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 |
-Validation report
Summary document | emd_28888_validation.pdf.gz | 868.5 KB | Display | EMDB validaton report |
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Full document | emd_28888_full_validation.pdf.gz | 868.1 KB | Display | |
Data in XML | emd_28888_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_28888_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28888 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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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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 |
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: 0.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
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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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 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
-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: |