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- EMDB-70128: ZnO Nucleated Z4-C3i Trimer Within the Octahedral Z4-Cage Nanoparticle -

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Basic information

Entry
Database: EMDB / ID: EMD-70128
TitleZnO Nucleated Z4-C3i Trimer Within the Octahedral Z4-Cage Nanoparticle
Map dataSharpened Map
Sample
  • Complex: ZnO Nucleated Z4-C3i Trimer Within the Octahedral Z4-Cage Nanoparticle
    • Protein or peptide: Z4-Cage Nanoparticle
  • Ligand: water
KeywordsZ4-C3i / ZnO / Z4-cage / Zinc Oxide / DE NOVO PROTEIN / nanoparticle / octahedral / hybrid nanomaterial / Zinc
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBorst AJ
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: De novo design of metal-oxide templating proteins
Authors: Saragovi A / Pyles H / Borst AJ / Baker D
History
DepositionApr 9, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70128.png

Downloads & links

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Map

FileDownload / File: emd_70128.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 480 pix.
= 424.8 Å		0.89 Å/pix.
x 480 pix.
= 424.8 Å		0.89 Å/pix.
x 480 pix.
= 424.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.109
Minimum - Maximum-0.8053179 - 1.1773618
Average (Standard dev.)0.00007134842 (±0.014428378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 424.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened

Fileemd_70128_additional_1.map
Annotationunsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer

Fileemd_70128_additional_2.map
AnnotationDeepEMhancer
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_70128_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_70128_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ZnO Nucleated Z4-C3i Trimer Within the Octahedral Z4-Cage Nanoparticle

EntireName: ZnO Nucleated Z4-C3i Trimer Within the Octahedral Z4-Cage Nanoparticle
Components
  • Complex: ZnO Nucleated Z4-C3i Trimer Within the Octahedral Z4-Cage Nanoparticle
    • Protein or peptide: Z4-Cage Nanoparticle
  • Ligand: water

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Supramolecule #1: ZnO Nucleated Z4-C3i Trimer Within the Octahedral Z4-Cage Nanoparticle

SupramoleculeName: ZnO Nucleated Z4-C3i Trimer Within the Octahedral Z4-Cage Nanoparticle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Symmetry expanded, 3D classified, and locally refined map of the Z4-cage focused on a Z4-C3i trimer that displays evidence of ZnO nucleation.
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Z4-Cage Nanoparticle

MacromoleculeName: Z4-Cage Nanoparticle / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 33.235766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKEGSAWSH PQFEKGGSGS DSTVLSKAIS VISTIARTSG SEEALRQAIE AVAEIAKEAQ DPTVLSKALE AITKILFTSI DNEEVARQA REAVLELSQD EETRELLEKL REAEDEEEKR EIIEELAKRG PEAILALLAE AIILGLDVEE VLDIAIEINK K DSDAASLL ...String:
MSKEGSAWSH PQFEKGGSGS DSTVLSKAIS VISTIARTSG SEEALRQAIE AVAEIAKEAQ DPTVLSKALE AITKILFTSI DNEEVARQA REAVLELSQD EETRELLEKL REAEDEEEKR EIIEELAKRG PEAILALLAE AIILGLDVEE VLDIAIEINK K DSDAASLL ITAISELARQ KGTEESLERA IRRIALLAIE AKDSTVLSKA ISVISTIART SGSEEALRLA IEAVALIALG GE DTVPARY IKISFEAELA GLDTKRLLEE GPKLYPELSI PDLMAIALFT HLHLDPYFLY RLLQQSR

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 61 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1332943
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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