+Open data
-Basic information
Entry | Database: PDB / ID: 8gel | ||||||
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Title | Cryo-EM structure of synthetic tetrameric building block sC4 | ||||||
Components | sC4 | ||||||
Keywords | DE NOVO PROTEIN / synthetic / tetramer / self-assembling | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Redler, R.L. / Huddy, T.F. / Hsia, Y. / Baker, D. / Ekiert, D. / Bhabha, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2024 Title: Blueprinting extendable nanomaterials with standardized protein blocks. Authors: Timothy F Huddy / Yang Hsia / Ryan D Kibler / Jinwei Xu / Neville Bethel / Deepesh Nagarajan / Rachel Redler / Philip J Y Leung / Connor Weidle / Alexis Courbet / Erin C Yang / Asim K Bera / ...Authors: Timothy F Huddy / Yang Hsia / Ryan D Kibler / Jinwei Xu / Neville Bethel / Deepesh Nagarajan / Rachel Redler / Philip J Y Leung / Connor Weidle / Alexis Courbet / Erin C Yang / Asim K Bera / Nicolas Coudray / S John Calise / Fatima A Davila-Hernandez / Hannah L Han / Kenneth D Carr / Zhe Li / Ryan McHugh / Gabriella Reggiano / Alex Kang / Banumathi Sankaran / Miles S Dickinson / Brian Coventry / T J Brunette / Yulai Liu / Justas Dauparas / Andrew J Borst / Damian Ekiert / Justin M Kollman / Gira Bhabha / David Baker / Abstract: A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The ...A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight 'train track' assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to 'back of an envelope' architectural blueprints. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gel.cif.gz | 331.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gel.ent.gz | 274.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/8gel ftp://data.pdbj.org/pub/pdb/validation_reports/ge/8gel | HTTPS FTP |
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-Related structure data
Related structure data | 29974MC 8g9jC 8g9kC 8ga6C 8ga7C 8tl7C 8v2dC 8v3bC M: map data used to model this data C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 57826.109 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: De novo designed tetramer sC4 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: synthetic construct (others) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: blot time = 4s |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.6 sec. / Electron dose: 47.07 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3850 |
EM imaging optics | Energyfilter slit width: 30 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3781336 | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 378829 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 224.3 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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