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	Growth Process of Fe-O Nanoclusters with Different Sizes Biosynthesized by Protein Nanocages.
Journal, issue, pages	J Am Chem Soc, Vol. 146, Issue 17, Page 11657-11668, Year 2024
Publish date	May 1, 2024
Authors	Wenming Wang / Hongfang Xi / Dan Fu / Danyang Ma / Wenjun Gong / Yaqin Zhao / Xiaomei Li / Lijie Wu / Yu Guo / Guanghua Zhao / Hongfei Wang /
PubMed Abstract	All protein-directed syntheses of metal nanoclusters (NCs) and nanoparticles (NPs) have attracted considerable attention because protein scaffolds provide a unique metal coordination environment and ...All protein-directed syntheses of metal nanoclusters (NCs) and nanoparticles (NPs) have attracted considerable attention because protein scaffolds provide a unique metal coordination environment and can adjust the shape and morphology of NCs and NPs. However, the detailed formation mechanisms of NCs or NPs directed by protein templates remain unclear. In this study, by taking advantage of the ferritin nanocage as a biotemplate to monitor the growth of Fe-O NCs as a function of time, we synthesized a series of iron NCs with different sizes and shapes and subsequently solved their corresponding three-dimensional atomic-scale structures by X-ray protein crystallography and cryo-electron microscopy. The time-dependent structure analyses revealed the growth process of these Fe-O NCs with the 4-fold channel of ferritin as nucleation sites. To our knowledge, the newly biosynthesized FeOGlu represents the largest Fe-O NCs with a definite atomic structure. This study contributes to our understanding of the formation mechanism of iron NCs and provides an effective method for metal NC synthesis.
External links	J Am Chem Soc / PubMed:38641862
Methods	EM (single particle) / X-ray diffraction
Resolution	2.059 - 3.2 Å
Structure data	37754 8wqu EMDB-37754, PDB-8wqu: Fe-O nanocluster of form-IX in the 4-fold channel of Ureaplasma diversum ferritin Method: EM (single particle) / Resolution: 2.8 Å 37755 8wqv EMDB-37755, PDB-8wqv: Fe-O nanocluster of form-VIII in the 4-fold channel of Ureaplasma diversum ferritin Method: EM (single particle) / Resolution: 2.7 Å 37757 8wqx EMDB-37757, PDB-8wqx: Fe-O nanocluster of form-X in the 4-fold channel of Ureaplasma diversum ferritin Method: EM (single particle) / Resolution: 3.2 Å 37758 8wqy EMDB-37758, PDB-8wqy: Fe-O nanocluster of form-XI in the 4-fold channel of Ureaplasma diversum ferritin Method: EM (single particle) / Resolution: 3.0 Å 37759 8wr0 EMDB-37759, PDB-8wr0: Fe-O nanocluster of form-XII in the 4-fold channel of Ureaplasma diversum ferritin Method: EM (single particle) / Resolution: 3.1 Å PDB-8w6m: Native strucutre of ferritin from Ureaplasma diversum Method: X-RAY DIFFRACTION / Resolution: 2.501 Å PDB-8w6q: ferritin from Ureaplasma diversum soaking in Fe2+ solution for 0 min Method: X-RAY DIFFRACTION / Resolution: 2.101 Å PDB-8w6s: Ferritin from Ureaplasma diversum soaking in Fe2+ solution for 2 min Method: X-RAY DIFFRACTION / Resolution: 2.099 Å PDB-8w6u: Ferritin from Ureaplasma diversum soaking in Fe2+ solution for 5 min Method: X-RAY DIFFRACTION / Resolution: 2.099 Å PDB-8w6y: Ferritin from Ureaplasma diversum soaking in Fe2+ solution for 10 min Method: X-RAY DIFFRACTION / Resolution: 2.502 Å PDB-8w73: Fe-O nanocluster of form-I in the 4-fold channel of Ureaplasma diversum ferritin Method: X-RAY DIFFRACTION / Resolution: 2.601 Å PDB-8w74: Fe-O nanocluster of form-II in the 4-fold channel of Ureaplasma diversum ferritin Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-8w79: Fe-O nanocluster of form-III in the 4-fold channel of Ureaplasma diversum ferritin Method: X-RAY DIFFRACTION / Resolution: 2.697 Å PDB-8w7b: Fe-O nanocluster of form-IV in the 4-fold channel of Ureaplasma diversum ferritin Method: X-RAY DIFFRACTION / Resolution: 2.7 Å PDB-8w7o: Fe-O nanocluster of form-V in the 4-fold channel of Ureaplasma diversum ferritin Method: X-RAY DIFFRACTION / Resolution: 2.399 Å PDB-8w7q: Fe-O nanocluster of form-VI in the 4-fold channel of Ureaplasma diversum ferritin Method: X-RAY DIFFRACTION / Resolution: 2.1 Å PDB-8w7t: Fe-O nanocluster of form-VII in the 4-fold channel of Ureaplasma diversum ferritin Method: X-RAY DIFFRACTION / Resolution: 2.499 Å PDB-8w7u: Mutant of ferritin from Ureaplasma diversum (Udif-E164A-E168A) without soaking Method: X-RAY DIFFRACTION / Resolution: 2.502 Å PDB-8w7v: Udif-E164A-E168A soaking in Fe2+ solution for 50 minutes Method: X-RAY DIFFRACTION / Resolution: 2.805 Å PDB-8wpt: Truncated mutant (1-171) of ferritin from Ureaplasma diversum Method: X-RAY DIFFRACTION / Resolution: 2.36 Å PDB-8wpv: Truncated mutant (1-171) of ferritin from Ureaplasma diversum soaked in Fe2+ solution for 30min Method: X-RAY DIFFRACTION / Resolution: 2.059 Å
Chemicals	ChemComp-FE: Unknown entry ChemComp-MG: Unknown entry ChemComp-CL: Unknown entry ChemComp-HOH: WATER
Source	ureaplasma diversum (bacteria)
Keywords	METAL BINDING PROTEIN / Ferritin / Iron / Fe-O cluster / 4-fold channel cavity / Ureaplasma diversum