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- EMDB-21325: Focused Classification of FIP200 NTD -

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Basic information

Entry
Database: EMDB / ID: EMD-21325
TitleFocused Classification of FIP200 NTD
Map dataFinal FIP200 NTD Map
Sample
  • Complex: FIP200 NTD Focused Classification Monomer
Function / homology
Function and homology information


Atg1/ULK1 kinase complex / ribophagy / glycophagy / phagophore assembly site membrane / pexophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / Macroautophagy ...Atg1/ULK1 kinase complex / ribophagy / glycophagy / phagophore assembly site membrane / pexophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phagophore assembly site / reticulophagy / Macroautophagy / autophagosome membrane / autophagosome assembly / positive regulation of cell size / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / positive regulation of autophagy / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / liver development / autophagy / heart development / nuclear membrane / defense response to virus / molecular adaptor activity / lysosome / negative regulation of cell population proliferation / innate immune response / endoplasmic reticulum membrane / protein kinase binding / cytosol
Similarity search - Function
Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11
Similarity search - Domain/homology
RB1-inducible coiled-coil protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsYokom AL / Shi X / Hurley JH
CitationJournal: J Cell Biol / Year: 2020
Title: ULK complex organization in autophagy by a C-shaped FIP200 N-terminal domain dimer.
Authors: Xiaoshan Shi / Adam L Yokom / Chunxin Wang / Lindsey N Young / Richard J Youle / James H Hurley /
Abstract: The autophagy-initiating human ULK complex consists of the kinase ULK1/2, FIP200, ATG13, and ATG101. Hydrogen-deuterium exchange mass spectrometry was used to map their mutual interactions. The N- ...The autophagy-initiating human ULK complex consists of the kinase ULK1/2, FIP200, ATG13, and ATG101. Hydrogen-deuterium exchange mass spectrometry was used to map their mutual interactions. The N-terminal 640 residues (NTD) of FIP200 interact with the C-terminal IDR of ATG13. Mutations in these regions abolish their interaction. Negative stain EM and multiangle light scattering showed that FIP200 is a dimer, while a single molecule each of the other subunits is present. The FIP200NTD is flexible in the absence of ATG13, but in its presence adopts the shape of the letter C ∼20 nm across. The ULK1 EAT domain interacts loosely with the NTD dimer, while the ATG13:ATG101 HORMA dimer does not contact the NTD. Cryo-EM of the NTD dimer revealed a structural similarity to the scaffold domain of TBK1, suggesting an evolutionary similarity between the autophagy-initiating TBK1 kinase and the ULK1 kinase complex.
History
DepositionFeb 4, 2020-
Header (metadata) releaseMar 18, 2020-
Map releaseJun 24, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21325.png

Downloads & links

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Map

FileDownload / File: emd_21325.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal FIP200 NTD Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.27 Å/pix.
x 180 pix.
= 409.32 Å		2.27 Å/pix.
x 180 pix.
= 409.32 Å		2.27 Å/pix.
x 180 pix.
= 409.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.274 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1 / Movie #1: 1
Minimum - Maximum-2.8269467 - 7.6950583
Average (Standard dev.)0.0021424736 (±0.06619328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 409.31998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2742.2742.274
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z409.320409.320409.320
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-2.8277.6950.002

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Supplemental data

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Half map: Half Map B

Fileemd_21325_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_21325_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FIP200 NTD Focused Classification Monomer

EntireName: FIP200 NTD Focused Classification Monomer
Components
  • Complex: FIP200 NTD Focused Classification Monomer

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Supramolecule #1: FIP200 NTD Focused Classification Monomer

SupramoleculeName: FIP200 NTD Focused Classification Monomer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK293T

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 20 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29198
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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