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- EMDB-62169: Cryo-EM structure of C3 symmetric interface of designed zinc-indu... -

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Basic information

Entry
Database: EMDB / ID: EMD-62169
TitleCryo-EM structure of C3 symmetric interface of designed zinc-induced tetrahedron Cage-t32-Zn1-HEHE-34
Map data
Sample
  • Complex: Cage-t32-Zn1-HEHE-34
    • Protein or peptide: Cage-t32-Zn1-HEHE-34
  • Ligand: ZINC ION
KeywordsZinc-binding protein / METAL BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsQu YN / Cao LX
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: De novo design of metal ion regulated protein assemblies
Authors: Qu YN / Cao LX
History
DepositionOct 24, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62169.png

Downloads & links

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Map

FileDownload / File: emd_62169.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 258.552 Å		1.08 Å/pix.
x 240 pix.
= 258.552 Å		1.08 Å/pix.
x 240 pix.
= 258.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-8.791086 - 13.618417000000001
Average (Standard dev.)0.0029462287 (±0.22440252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 258.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62169_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62169_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cage-t32-Zn1-HEHE-34

EntireName: Cage-t32-Zn1-HEHE-34
Components
  • Complex: Cage-t32-Zn1-HEHE-34
    • Protein or peptide: Cage-t32-Zn1-HEHE-34
  • Ligand: ZINC ION

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Supramolecule #1: Cage-t32-Zn1-HEHE-34

SupramoleculeName: Cage-t32-Zn1-HEHE-34 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Cage-t32-Zn1-HEHE-34

MacromoleculeName: Cage-t32-Zn1-HEHE-34 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 27.724348 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH SSGLEVLFQG PGGTMEKLKE IVKHLEVAIK YLKEGKVDLA DLVVADAIEL AKEAGDKASL EILKVAHKAI DTLGREGKL EEAAKIVKYA KEYVEAKIKG DREKLRELLE KVKKDVLEAI KKGDEEFYEA LVKIARIIAE DLGDEKSLKV L EALEEFFK ...String:
MGHHHHHHHH SSGLEVLFQG PGGTMEKLKE IVKHLEVAIK YLKEGKVDLA DLVVADAIEL AKEAGDKASL EILKVAHKAI DTLGREGKL EEAAKIVKYA KEYVEAKIKG DREKLRELLE KVKKDVLEAI KKGDEEFYEA LVKIARIIAE DLGDEKSLKV L EALEEFFK EWKRLEKEGK SLDEKLHLFL RVGERLLEIG DKESLEMLIE LLEELAKEIK KAGNEELLVR AEAAIKDIRK HI KEL

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 535381
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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