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- EMDB-62165: Cryo-EM structure of designed zinc-induced icosahedron Cage-i53-Z... -

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Basic information

Entry
Database: EMDB / ID: EMD-62165
TitleCryo-EM structure of designed zinc-induced icosahedron Cage-i53-Zn1-HEHE-6
Map data
Sample
  • Complex: Cage-i53-Zn1-HEHE-6
    • Protein or peptide: Cage-i53-Zn1-HEHE-6
  • Ligand: ZINC ION
KeywordsZinc-binding protein / METAL BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 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_62165.png

Downloads & links

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Map

FileDownload / File: emd_62165.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.38527802 - 0.64282876
Average (Standard dev.)0.00018555511 (±0.024672208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62165_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_62165_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-i53-Zn1-HEHE-6

EntireName: Cage-i53-Zn1-HEHE-6
Components
  • Complex: Cage-i53-Zn1-HEHE-6
    • Protein or peptide: Cage-i53-Zn1-HEHE-6
  • Ligand: ZINC ION

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Supramolecule #1: Cage-i53-Zn1-HEHE-6

SupramoleculeName: Cage-i53-Zn1-HEHE-6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.748 MDa

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Macromolecule #1: Cage-i53-Zn1-HEHE-6

MacromoleculeName: Cage-i53-Zn1-HEHE-6 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 31.438463 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH SSGLEVLFQG PGGTVVEEVR RFAEELAEEV LRVGGEAMRP YAEMVRHLGE AAVAALEGRA EEADRLVRDV LEMAREVGA EGLARLLERV HREARELLRE GRREEAAALV LAAALAAGAV AVAEAYVRLG QPIRLIAEYV AERLVELAEL L RRLGVPLR ...String:
MGHHHHHHHH SSGLEVLFQG PGGTVVEEVR RFAEELAEEV LRVGGEAMRP YAEMVRHLGE AAVAALEGRA EEADRLVRDV LEMAREVGA EGLARLLERV HREARELLRE GRREEAAALV LAAALAAGAV AVAEAYVRLG QPIRLIAEYV AERLVELAEL L RRLGVPLR RIIRLLEEVL RVVAEALRRA GVPEPEIRKV EAAAYIRLAA YLLRQLGYEA LAKRLLEARE LLLEGRVEEA AH LLEDVYA LFHREIERLG FEAPEELRVA DLLLARAIAL IKAI

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 120 / 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 GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.0 µm / Nominal defocus min: 1.5 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: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66846
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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