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- EMDB-53556: Human FAM118B(24-334) hexameric filament -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53556
TitleHuman FAM118B(24-334) hexameric filament
Map data
Sample
  • Organelle or cellular component: Human FAM118B(24-334) hexameric filament
KeywordsNADase / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsBaretic D / Missoury S / Coste F / Patel K / Delarue M / Ahel I / Suskiewicz MJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human FAM118B(24-334) hexameric filament
Authors: Missoury S / Baretic D / Coste F / Patel K / Delarue M / Ahel I / Suskiewicz MJ
History
DepositionMay 5, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53556.png

Downloads & links

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Map

FileDownload / File: emd_53556.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 512 pix.
= 429.568 Å		0.84 Å/pix.
x 512 pix.
= 429.568 Å		0.84 Å/pix.
x 512 pix.
= 429.568 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.225
Minimum - Maximum-0.38476887 - 0.4712553
Average (Standard dev.)-0.000030508587 (±0.017573783)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 429.568 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53556_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_53556_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 : Human FAM118B(24-334) hexameric filament

EntireName: Human FAM118B(24-334) hexameric filament
Components
  • Organelle or cellular component: Human FAM118B(24-334) hexameric filament

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Supramolecule #1: Human FAM118B(24-334) hexameric filament

SupramoleculeName: Human FAM118B(24-334) hexameric filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

Concentration0.1 mg/mL
BufferpH: 8.8 / Details: 25 mM Tris, pH 8.8, 250 mM NaCl, 0.5 mM TCEP
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 40.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 348508
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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