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- EMDB-46934: local refinement of arpC5, arpC1 and arp2 for arp 2/3 complex 2 N... -

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Basic information

Entry
Database: EMDB / ID: EMD-46934
Titlelocal refinement of arpC5, arpC1 and arp2 for arp 2/3 complex 2 NPFs bound and arpC5 tail mostly dissociated
Map datalocal refinement of arpC5, arpC1 and arp2 for arp 2/3 complex 2 NPFs bound and arpC5 tail mostly dissociated
Sample
  • Complex: Arp 2/3 complex bound to NPFs
Keywordsactin / arp 2-3 complex / N-WASP / nucleation promoting factor / STRUCTURAL PROTEIN
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsSaks AJ / Barrie KR / Dominguez R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM073791-19 United States
CitationJournal: To Be Published
Title: Arp 2/3 complex with bound NPFs
Authors: Saks AJ / Barrie KR / Dominguez R
History
DepositionSep 6, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46934.png

Downloads & links

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Map

FileDownload / File: emd_46934.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refinement of arpC5, arpC1 and arp2 for arp 2/3 complex 2 NPFs bound and arpC5 tail mostly dissociated
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.09488513 - 0.25426483
Average (Standard dev.)0.00030376876 (±0.006071257)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 302.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46934_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_46934_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_46934_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Arp 2/3 complex bound to NPFs

EntireName: Arp 2/3 complex bound to NPFs
Components
  • Complex: Arp 2/3 complex bound to NPFs

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Supramolecule #1: Arp 2/3 complex bound to NPFs

SupramoleculeName: Arp 2/3 complex bound to NPFs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Bos taurus (domestic cattle)
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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: OTHER / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 161035
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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