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- EMDB-37758: Fe-O nanocluster of form-XI in the 4-fold channel of Ureaplasma d... -

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Basic information

Entry
Database: EMDB / ID: EMD-37758
TitleFe-O nanocluster of form-XI in the 4-fold channel of Ureaplasma diversum ferritin
Map data
Sample
  • Complex: ferritin
    • Protein or peptide: ferritin
  • Ligand: FE (III) ION
  • Ligand: water
Keywordsferritin / METAL BINDING PROTEIN
Biological speciesUreaplasma diversum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWang WM / Ma DY / Gong WJ / Wu LJ / Wang HF
Funding support China, 1 items
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, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37758.png

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Map

FileDownload / File: emd_37758.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 268.006 Å		1.05 Å/pix.
x 256 pix.
= 268.006 Å		1.05 Å/pix.
x 256 pix.
= 268.006 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0469 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.437
Minimum - Maximum-1.0476086 - 2.028192
Average (Standard dev.)0.0029387004 (±0.116931856)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 268.0064 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37758_half_map_1.map
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Half map: #2

Fileemd_37758_half_map_2.map
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Sample components

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Entire : ferritin

EntireName: ferritin
Components
  • Complex: ferritin
    • Protein or peptide: ferritin
  • Ligand: FE (III) ION
  • Ligand: water

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Supramolecule #1: ferritin

SupramoleculeName: ferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Ureaplasma diversum (bacteria)

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Macromolecule #1: ferritin

MacromoleculeName: ferritin / type: protein_or_peptide / ID: 1 / Details: WP_081847832.1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Ureaplasma diversum (bacteria)
Molecular weightTheoretical: 21.254996 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLYRERNNIM QKSNKINDAL NQHYKLNVEL GLVYAHYAHV ADDEFDMPYL GKFIQHLSED KLGVHKEYIS DYFKRNGMKL KTDVSVAVK SIPSDAKALI QEVYARENEV RDHVKAIAKL ALAEDDYESF YFIQWYVRDG LKDLTEVDDV VKLFNSSNDK L IIEETIKE MVEKEESEHE IWG

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 10 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8w6m

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11289
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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