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- PDB-8wqu: Fe-O nanocluster of form-IX in the 4-fold channel of Ureaplasma d... -

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Basic information

Entry
Database: PDB / ID: 8wqu
TitleFe-O nanocluster of form-IX in the 4-fold channel of Ureaplasma diversum ferritin
Componentsferritin
KeywordsMETAL BINDING PROTEIN / ferritin
Function / homology:
Function and homology information
Biological speciesUreaplasma diversum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWang, W.M. / Ma, D.Y. / Gong, W.J. / Wu, L.J. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)62075118, 21601112 China
CitationJournal: J Am Chem Soc / Year: 2024
Title: Growth Process of Fe-O Nanoclusters with Different Sizes Biosynthesized by Protein Nanocages.
Authors: Wenming Wang / Hongfang Xi / Dan Fu / Danyang Ma / Wenjun Gong / Yaqin Zhao / Xiaomei Li / Lijie Wu / Yu Guo / Guanghua Zhao / Hongfei Wang /
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.
History
DepositionOct 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ferritin
B: ferritin
C: ferritin
D: ferritin
E: ferritin
F: ferritin
G: ferritin
H: ferritin
I: ferritin
J: ferritin
K: ferritin
L: ferritin
M: ferritin
N: ferritin
O: ferritin
P: ferritin
Q: ferritin
R: ferritin
S: ferritin
T: ferritin
U: ferritin
V: ferritin
W: ferritin
X: ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,46048
Polymers510,12024
Non-polymers1,34024
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
ferritin / ferritin-like domain-containing protein


Mass: 21254.996 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Details: WP_081847832.1 / Source: (gene. exp.) Ureaplasma diversum (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ferritin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Ureaplasma diversum (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.15.2_3472: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5321 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00633408
ELECTRON MICROSCOPYf_angle_d0.59845144
ELECTRON MICROSCOPYf_dihedral_angle_d5.64127792
ELECTRON MICROSCOPYf_chiral_restr0.0424896
ELECTRON MICROSCOPYf_plane_restr0.0045808

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