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- EMDB-60619: Tubular PuuE complex with C6 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-60619
TitleTubular PuuE complex with C6 symmetry
Map data
Sample
  • Complex: Tubular PuuE complex with C6 symmetry
KeywordsSupramolecular complex / DE NOVO PROTEIN
Biological speciesPseudomonas fluorescens (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 17.5 Å
AuthorsNoji M / Sugita Y / Suzuki Y
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR22A7 Japan
Japan Society for the Promotion of Science (JSPS)21H05116 Japan
Japan Society for the Promotion of Science (JSPS)21H05117 Japan
Japan Society for the Promotion of Science (JSPS)19K22253 Japan
Japan Society for the Promotion of Science (JSPS)19H02832 Japan
CitationJournal: To Be Published
Title: Protein design of two-component tubular assemblies like cytoskeletons
Authors: Noji M / Sugita Y / Yamazaki Y / Miyazaki M / Suzuki Y
History
DepositionJun 21, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60619.png

Downloads & links

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Map

FileDownload / File: emd_60619.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.66 Å/pix.
x 220 pix.
= 805.2 Å		3.66 Å/pix.
x 220 pix.
= 805.2 Å		3.66 Å/pix.
x 220 pix.
= 805.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.03178891 - 0.05502012
Average (Standard dev.)0.00004297967 (±0.009444101)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 805.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60619_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60619_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_60619_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 : Tubular PuuE complex with C6 symmetry

EntireName: Tubular PuuE complex with C6 symmetry
Components
  • Complex: Tubular PuuE complex with C6 symmetry

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Supramolecule #1: Tubular PuuE complex with C6 symmetry

SupramoleculeName: Tubular PuuE complex with C6 symmetry / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas fluorescens (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 77.7 Å
Applied symmetry - Helical parameters - Δ&Phi: 32.6 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 17.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 39841
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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