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- EMDB-33421: Pinhead of human centrioles from HeLa cells. -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-33421
TitlePinhead of human centrioles from HeLa cells.
Map dataPostprocessed map of pinhead of human centrioles from HeLa cells.
Sample
  • Organelle or cellular component: Microtubule triplets with complete C tubule of human centrioles from HeLa cells.
KeywordsComplex / Centriole / Microtubule / in situ / CELL CYCLE
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 31.0 Å
AuthorsLi SG / Wang ZY / Zhu Y / Ji G / Sun F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31830020 China
CitationJournal: Nat.Methods / Year: 2023
Title: ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study
Authors: Li SG / Wang ZY / Jia X / Niu TX / Zhang JG / Yin GL / Zhang XY / Zhu Y / Ji G / Sun F
History
DepositionMay 11, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33421.png

Downloads & links

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Map

FileDownload / File: emd_33421.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of pinhead of human centrioles from HeLa cells.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.6 Å/pix.
x 72 pix.
= 619.2 Å		8.6 Å/pix.
x 72 pix.
= 619.2 Å		8.6 Å/pix.
x 72 pix.
= 619.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.193
Minimum - Maximum-0.54693735 - 1.2276647
Average (Standard dev.)0.019856986 (±0.12302669)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 619.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33421_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of pinhead of human centrioles from HeLa cells.

Fileemd_33421_half_map_1.map
AnnotationHalf map of pinhead of human centrioles from HeLa cells.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of pinhead of human centrioles from HeLa cells.

Fileemd_33421_half_map_2.map
AnnotationHalf map of pinhead of human centrioles from HeLa cells.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Microtubule triplets with complete C tubule of human centrioles f...

EntireName: Microtubule triplets with complete C tubule of human centrioles from HeLa cells.
Components
  • Organelle or cellular component: Microtubule triplets with complete C tubule of human centrioles from HeLa cells.

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Supramolecule #1: Microtubule triplets with complete C tubule of human centrioles f...

SupramoleculeName: Microtubule triplets with complete C tubule of human centrioles from HeLa cells.
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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 31.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1148
ExtractionNumber tomograms: 59 / Number images used: 4818
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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