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- EMDB-4268: Abp1-SNAP bound to Arp2/3 complex (class 2) -

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Basic information

Entry
Database: EMDB / ID: 4268
TitleAbp1-SNAP bound to Arp2/3 complex (class 2)
Map dataArp2/3 complex with bound dimer of Abp1
SampleArp2/3 complex with bound Abp1 dimer:
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / 21 Å resolution
AuthorsSokolova OS / Goode BL
CitationJournal: Nat Commun / Year: 2018
Title: Abp1 promotes Arp2/3 complex-dependent actin nucleation and stabilizes branch junctions by antagonizing GMF.
Authors: Siyang Guo / Olga S Sokolova / Johnson Chung / Shae Padrick / Jeff Gelles / Bruce L Goode
DateDeposition: Jan 23, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Mar 20, 2019 / Last update: Mar 20, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4268.map.gz (map file in CCP4 format, 4001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
2.5 Å/pix.
= 250. Å
100 pix
2.5 Å/pix.
= 250. Å
100 pix
2.5 Å/pix.
= 250. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density
Contour Level:0.18 (by author), 0.18 (movie #1):
Minimum - Maximum-0.53692555 - 1.7988012
Average (Standard dev.)0.02087207 (0.124266855)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin-50.0-50.0-50.0
Limit49.049.049.0
Spacing100100100
CellA=B=C: 250.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z250.000250.000250.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-0.5371.7990.021

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Supplemental data

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Sample components

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Entire Arp2/3 complex with bound Abp1 dimer

EntireName: Arp2/3 complex with bound Abp1 dimer / Number of components: 1

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Component #1: cellular-component, Arp2/3 complex with bound Abp1 dimer

Cellular-componentName: Arp2/3 complex with bound Abp1 dimer / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionpH: 7.5
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2100
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 13 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 1000 (2k x 2k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 3500
3D reconstructionResolution: 21 Å / Resolution method: FSC 0.5 CUT-OFF

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