+Open data
-Basic information
Entry | Database: PDB / ID: 8v3b | ||||||
---|---|---|---|---|---|---|---|
Title | Computational Designed Nanocage O43_129_+4 | ||||||
Components |
| ||||||
Keywords | DE NOVO PROTEIN / O43 / Nanocage / De Novo / Programmable Design | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.4 Å | ||||||
Authors | Carr, K.D. / Weidle, C. / Borst, A.J. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8v3b.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8v3b.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 8v3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/8v3b ftp://data.pdbj.org/pub/pdb/validation_reports/v3/8v3b | HTTPS FTP |
---|
-Related structure data
Related structure data | 42944MC 8g9jC 8g9kC 8ga6C 8ga7C 8gelC 8tl7C 8v2dC M: map data used to model this data C: citing same article (ref.) |
---|
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 33976.965 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 46675.922 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Computational Designed Nanocage O43_129_+4 / Type: COMPLEX Details: Chain A and chain B were expressed separately in E. coli. Complex was formed by mixing the lysis of chain A and chain B. Sample was purified through HIS-tag on chain A. Entity ID: all / Source: RECOMBINANT | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: unidentified (others) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 8 / Details: 300mM NaCl, 25mM Tris-HCL | |||||||||||||||
Buffer component |
| |||||||||||||||
Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 23522 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: O (octahedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16878 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 804.6 / Protocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient Details: Computationally designed model was docked into experimentally derived volume map in ChimeraX. It was then relaxed using Namdinator. Then it was trimmed to polyA in PHENIX. |