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- EMDB-19626: Low resolution cryo-EM map of human ZNFX1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-19626
TitleLow resolution cryo-EM map of human ZNFX1
Map dataMain map sharpened (B -738 A^2)
Sample
  • Complex: Recombinant full-length human ZNFX1
KeywordsHelicase / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.62 Å
AuthorsGrabarczyk DB / Ehrmann JF / Kurzbauer R / Clausen T
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission847548European Union
CitationJournal: To Be Published
Title: Antiviral mechanism of the non-canonical ubiquitin ligase ZNFX1
Authors: Grabarczyk DB / Clausen T
History
DepositionFeb 14, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19626.png

Downloads & links

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Map

FileDownload / File: emd_19626.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map sharpened (B -738 A^2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.9 Å/pix.
x 100 pix.
= 190.2 Å		1.9 Å/pix.
x 100 pix.
= 190.2 Å		1.9 Å/pix.
x 100 pix.
= 190.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.902 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.4787817 - 1.8053901
Average (Standard dev.)0.005858062 (±0.061080568)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 190.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19626_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Main map not sharpened

Fileemd_19626_additional_1.map
AnnotationMain map not sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19626_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19626_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 : Recombinant full-length human ZNFX1

EntireName: Recombinant full-length human ZNFX1
Components
  • Complex: Recombinant full-length human ZNFX1

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Supramolecule #1: Recombinant full-length human ZNFX1

SupramoleculeName: Recombinant full-length human ZNFX1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 220 KDa

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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

Concentration0.4 mg/mL
BufferpH: 7.5 / Details: 25 mM HEPES pH 7.5 150 mM NaCl 0.5 mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1705619
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 12637
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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