Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Blueprinting extendable nanomaterials with standardized protein blocks.
Journal, issue, pages	Nature, Vol. 627, Issue 8005, Page 898-904, Year 2024
Publish date	Mar 13, 2024
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 /
PubMed 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.
External links	Nature / PubMed:38480887 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.48 - 12.98 Å
Structure data	29974 8gel EMDB-29974, PDB-8gel: Cryo-EM structure of synthetic tetrameric building block sC4 Method: EM (single particle) / Resolution: 3.9 Å EMDB-40070: Cryo-EM map of synthetic cage_O3_10 reconstructed without symmetry (C1) Method: EM (single particle) / Resolution: 7.4 Å EMDB-40071: Cryo-EM map of synthetic cage_O3_10 reconstructed with O symmetry Method: EM (single particle) / Resolution: 6.0 Å EMDB-40073: Cryo-EM map of synthetic cage_T3_5 reconstructed without symmetry (C1), with 1 monomer missing (class 3.0) Method: EM (single particle) / Resolution: 6.1 Å EMDB-40074: Cryo-EM map of synthetic cage_T3_5 reconstructed with T symmetry Method: EM (single particle) / Resolution: 3.6 Å EMDB-40075: Cryo-EM map of synthetic cage_T3_5 reconstructed without symmetry (C1) Method: EM (single particle) / Resolution: 4.3 Å EMDB-40076: Cryo-EM map of synthetic cage_T3_5+2 reconstructed without symmetry (C1) Method: EM (single particle) / Resolution: 6.7 Å 41364 8tl7 EMDB-41364, PDB-8tl7: CryoEM Structure of a Computationally Designed T3 Tetrahedral Nanocage Method: EM (single particle) / Resolution: 4.05 Å EMDB-41907: Computationally Designed, Expandable O4 Octahedral Handshake Nanocage Method: EM (single particle) / Resolution: 6.34 Å EMDB-42031: Computational Designed Nanocage O43_129_+8 Method: EM (single particle) / Resolution: 12.98 Å 42906 8v2d EMDB-42906, PDB-8v2d: Computational Designed Nanocage O43_129 Method: EM (single particle) / Resolution: 6.77 Å 42944 8v3b EMDB-42944, PDB-8v3b: Computational Designed Nanocage O43_129_+4 Method: EM (single particle) / Resolution: 6.4 Å EMDB-43318: Twistless helix 12 repeat ring design R12B Method: EM (single particle) / Resolution: 5.2 Å PDB-8g9j: Geometrically programmable nanomaterial construction using regularized protein building blocks Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-8g9k: Geometrically programmable nanomaterial construction using regularized protein building blocks Method: X-RAY DIFFRACTION / Resolution: 2.48 Å PDB-8ga6: Geometrically programmable nanomaterial construction using regularized protein building blocks Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-8ga7: Geometrically programmable nanomaterial construction using regularized protein building blocks Method: X-RAY DIFFRACTION / Resolution: 2.93 Å
Chemicals	ChemComp-HOH: WATER / Water
Source	synthetic construct (others) unidentified (others)
Keywords	DE NOVO PROTEIN / nanomaterial / protein building blocks / De novo design / train-track / synthetic / tetramer / self-assembling / expandable nanomaterial / de novo / t3 tetrahedral nanocage / computationally designed / nanocage / expandable nanomaterials / O43_129 / extendable nanomaterials / O43 / Programmable Design