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- EMDB-8899: Negative stain reconstruction of human autophagy associated prote... -

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Basic information

Entry
Database: EMDB / ID: 8899
TitleNegative stain reconstruction of human autophagy associated protein complex, ATG2A-WIPI4
SampleComplex between human ATG2A and WIPI4 proteins.
SourceHomo sapiens / human
Map dataNegative stain reconstruction of human ATG2A-WIPI4 complex
Methodsingle particle reconstruction, at 30.3 Å resolution
AuthorsChowdhury S / Otomo C / Leitner A / Ohashi K / Aebersold R / Lander GC / Otomo T
CitationTo be published

To be published Search PubMed
To be Published
Chowdhury S / Otomo C / Leitner A / Ohashi K / Aebersold R / Lander GC / Otomo T

DateDeposition: Aug 21, 2017 / Header (metadata) release: Sep 6, 2017 / Map release: Sep 6, 2017 / Last update: Sep 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.63
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 4.63
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8899.map.gz (map file in CCP4 format, 3539 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
4.1 Å/pix.
= 393.6 Å
96 pix
4.1 Å/pix.
= 393.6 Å
96 pix
4.1 Å/pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.1 Å
Density
Contour Level:4.63 (by author), 4.63 (movie #1):
Minimum - Maximum-6.5388603 - 16.379532
Average (Standard dev.)0.061396632 (0.7330839)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin000
Limit959595
Spacing969696
CellA=B=C: 393.59998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-6.53916.3800.061

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Supplemental data

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Sample components

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Entire Complex between human ATG2A and WIPI4 proteins.

EntireName: Complex between human ATG2A and WIPI4 proteins. / Details: Full length proteins / Number of components: 1
MassTheoretical: 250 kDa

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Component #1: protein, Complex between human ATG2A and WIPI4 proteins.

ProteinName: Complex between human ATG2A and WIPI4 proteins. / Details: Full length proteins / Recombinant expression: No
MassTheoretical: 250 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Spodoptera frugiperda / arthropod / Strain: 9

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.01 mg/ml / pH: 7.5
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 52000 X (nominal), 52000 X (calibrated) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 1500 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC / Temperature: K ( 273.15 - 298.15 K)
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1407 / Sampling size: 15.6 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 5317
3D reconstructionSoftware: Relion / Resolution: 30.3 Å / Resolution method: FSC 0.143 CUT-OFF

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