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- EMDB-63570: Local refinement map of TBCE-LRRD in the TBC-DE-Arl2-beta-tubulin... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-63570
TitleLocal refinement map of TBCE-LRRD in the TBC-DE-Arl2-beta-tubulin complex
Map data
Sample
  • Complex: Complex of tubulin specific chaperone D, E, Arl2 and beta-tubulin
Keywordschaperone / complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsSeong YJ / Kim HM / Byun KM / Park YW / Roh SH
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Science / Year: 2025
Title: Structural dissection of alpha beta-tubulin heterodimer assembly and disassembly by human tubulin-specific chaperones
Authors: Seong YJ / Kim HM / Byun KM / Park YW / Roh SH
History
DepositionFeb 26, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63570.png

Downloads & links

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Map

FileDownload / File: emd_63570.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.)
1.16 Å/pix.
x 360 pix.
= 417.204 Å		1.16 Å/pix.
x 360 pix.
= 417.204 Å		1.16 Å/pix.
x 360 pix.
= 417.204 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1589 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.4597899 - 2.2237346
Average (Standard dev.)-0.00042616087 (±0.02232008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 417.204 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63570_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_63570_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 : Complex of tubulin specific chaperone D, E, Arl2 and beta-tubulin

EntireName: Complex of tubulin specific chaperone D, E, Arl2 and beta-tubulin
Components
  • Complex: Complex of tubulin specific chaperone D, E, Arl2 and beta-tubulin

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Supramolecule #1: Complex of tubulin specific chaperone D, E, Arl2 and beta-tubulin

SupramoleculeName: Complex of tubulin specific chaperone D, E, Arl2 and beta-tubulin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 260 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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 714398
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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