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	Accurate computational design of three-dimensional protein crystals.
Journal, issue, pages	Nat Mater, Vol. 22, Issue 12, Page 1556-1563, Year 2023
Publish date	Oct 16, 2023
Authors	Zhe Li / Shunzhi Wang / Una Nattermann / Asim K Bera / Andrew J Borst / Muammer Y Yaman / Matthew J Bick / Erin C Yang / William Sheffler / Byeongdu Lee / Soenke Seifert / Greg L Hura / Hannah Nguyen / Alex Kang / Radhika Dalal / Joshua M Lubner / Yang Hsia / Hugh Haddox / Alexis Courbet / Quinton Dowling / Marcos Miranda / Andrew Favor / Ali Etemadi / Natasha I Edman / Wei Yang / Connor Weidle / Banumathi Sankaran / Babak Negahdari / Michael B Ross / David S Ginger / David Baker /
PubMed Abstract	Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing ...Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.
External links	Nat Mater / PubMed:37845322
Methods	EM (single particle) / X-ray diffraction
Resolution	1.85 - 5.53 Å
Structure data	27031 8cwy EMDB-27031, PDB-8cwy: Accurate computational design of genetically encoded 3D protein crystals Method: EM (single particle) / Resolution: 3.34 Å 40926 8szz EMDB-40926, PDB-8szz: CryoEM Structure of Computationally Designed Nanocage O32-ZL4 Method: EM (single particle) / Resolution: 2.9 Å PDB-8cus: Accurate computational design of genetically encoded 3D protein crystals Method: X-RAY DIFFRACTION / Resolution: 3.98 Å PDB-8cut: Accurate computational design of genetically encoded 3D protein crystals Method: X-RAY DIFFRACTION / Resolution: 4.0 Å PDB-8cuu: Accurate computational design of genetically encoded 3D protein crystals Method: X-RAY DIFFRACTION / Resolution: 2.91 Å PDB-8cuv: Accurate computational design of genetically encoded 3D protein crystals Method: X-RAY DIFFRACTION / Resolution: 2.8 Å PDB-8cuw: Accurate computational design of genetically encoded 3D protein crystals Method: X-RAY DIFFRACTION / Resolution: 3.55 Å PDB-8cux: Accurate computational design of genetically encoded 3D protein crystals Method: X-RAY DIFFRACTION / Resolution: 1.85 Å PDB-8cws: Accurate computational design of genetically encoded 3D protein crystals Method: X-RAY DIFFRACTION / Resolution: 4.4 Å PDB-8cwz: Accurate computational design of genetically encoded 3D protein crystals Method: X-RAY DIFFRACTION / Resolution: 5.53 Å PDB-8far: Accurate computational design of genetically encoded 3D protein crystals Method: X-RAY DIFFRACTION / Resolution: 3.66 Å
Chemicals	ChemComp-HOH: WATER / Water ChemComp-NA: Unknown entry
Source	Escherichia coli (E. coli) synthetic construct (others) thermotoga maritima (bacteria)
Keywords	DE NOVO PROTEIN / DE NOVO DESIGN / genetically encoded / 3D protein crystals / 3D crystals / nanocage / rosetta / cryoEM / O32-ZL4