+Open data
-Basic information
Entry | Database: PDB / ID: 8v2d | ||||||
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Title | Computational Designed Nanocage O43_129 | ||||||
Components |
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Keywords | DE NOVO PROTEIN / De Novo / Nanocage / O43_129 / extendable nanomaterials | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.77 Å | ||||||
Authors | Weidle, C. / Kibler, R.D. | ||||||
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 | 8v2d.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8v2d.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 8v2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8v2d_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8v2d_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8v2d_validation.xml.gz | 260 KB | Display | |
Data in CIF | 8v2d_validation.cif.gz | 463.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/8v2d ftp://data.pdbj.org/pub/pdb/validation_reports/v2/8v2d | HTTPS FTP |
-Related structure data
Related structure data | 42906MC 8g9jC 8g9kC 8ga6C 8ga7C 8gelC 8tl7C 8v3bC C: citing same article (ref.) M: map data used to model this data |
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-Links
-Assembly
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Noncrystallographic symmetry (NCS) | NCS domain:
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