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- EMDB-21876: Structure of human ATG9A, the only transmembrane protein of the c... -

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Basic information

Entry
Database: EMDB / ID: EMD-21876
TitleStructure of human ATG9A, the only transmembrane protein of the core autophagy machinery
Map data
Sample
  • Complex: Autophagy Related 9A with LMNG
    • Protein or peptide: Autophagy-related protein 9A
  • Ligand: Lauryl Maltose Neopentyl Glycol
KeywordsTG9A / autophagosome / autophagy / cryoEM / molecular dynamics / transmembrane protein / membranecurvature / cellular compartments / membrane morphology / lipids / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of macrophage cytokine production / phospholipid scramblase activity / protein localization to Golgi apparatus / programmed necrotic cell death / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / negative regulation of interferon-beta production / bone morphogenesis / phagophore assembly site ...negative regulation of macrophage cytokine production / phospholipid scramblase activity / protein localization to Golgi apparatus / programmed necrotic cell death / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / negative regulation of interferon-beta production / bone morphogenesis / phagophore assembly site / reticulophagy / Macroautophagy / autophagosome assembly / mitophagy / autophagosome / synaptic membrane / PINK1-PRKN Mediated Mitophagy / trans-Golgi network / recycling endosome / mitochondrial membrane / recycling endosome membrane / late endosome membrane / late endosome / endosome / Golgi membrane / innate immune response / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / membrane
Similarity search - Function
Autophagy-related protein 9 / Autophagy protein ATG9
Similarity search - Domain/homology
Autophagy-related protein 9A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGuardia CM / Tan X
CitationJournal: Cell Rep / Year: 2020
Title: Structure of Human ATG9A, the Only Transmembrane Protein of the Core Autophagy Machinery.
Authors: Carlos M Guardia / Xiao-Feng Tan / Tengfei Lian / Mitra S Rana / Wenchang Zhou / Eric T Christenson / Augustus J Lowry / José D Faraldo-Gómez / Juan S Bonifacino / Jiansen Jiang / Anirban Banerjee /
Abstract: Autophagy is a catabolic process involving capture of cytoplasmic materials into double-membraned autophagosomes that subsequently fuse with lysosomes for degradation of the materials by lysosomal ...Autophagy is a catabolic process involving capture of cytoplasmic materials into double-membraned autophagosomes that subsequently fuse with lysosomes for degradation of the materials by lysosomal hydrolases. One of the least understood components of the autophagy machinery is the transmembrane protein ATG9. Here, we report a cryoelectron microscopy structure of the human ATG9A isoform at 2.9-Å resolution. The structure reveals a fold with a homotrimeric domain-swapped architecture, multiple membrane spans, and a network of branched cavities, consistent with ATG9A being a membrane transporter. Mutational analyses support a role for the cavities in the function of ATG9A. In addition, structure-guided molecular simulations predict that ATG9A causes membrane bending, explaining the localization of this protein to small vesicles and highly curved edges of growing autophagosomes.
History
DepositionApr 29, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.538
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.538
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wr4
  • Surface level: 0.538
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21876.png

Downloads & links

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Map

FileDownload / File: emd_21876.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 192 pix.
= 203.52 Å		1.06 Å/pix.
x 192 pix.
= 203.52 Å		1.06 Å/pix.
x 192 pix.
= 203.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.538 / Movie #1: 0.538
Minimum - Maximum-4.1479135 - 6.7512074
Average (Standard dev.)0.00932175 (±0.15982066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 203.51999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z203.520203.520203.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-4.1486.7510.009

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Supplemental data

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Sample components

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Entire : Autophagy Related 9A with LMNG

EntireName: Autophagy Related 9A with LMNG
Components
  • Complex: Autophagy Related 9A with LMNG
    • Protein or peptide: Autophagy-related protein 9A
  • Ligand: Lauryl Maltose Neopentyl Glycol

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Supramolecule #1: Autophagy Related 9A with LMNG

SupramoleculeName: Autophagy Related 9A with LMNG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Autophagy-related protein 9A

MacromoleculeName: Autophagy-related protein 9A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 94.551031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQFDTEYQR LEASYSDSPP GEEDLLVHVA EGSKSPWHHI ENLDLFFSRV YNLHQKNGFT CMLIGEIFEL MQFLFVVAFT TFLVSCVDY DILFANKMVN HSLHPTEPVK VTLPDAFLPA QVCSARIQEN GSLITILVIA GVFWIHRLIK FIYNICCYWE I HSFYLHAL ...String:
MAQFDTEYQR LEASYSDSPP GEEDLLVHVA EGSKSPWHHI ENLDLFFSRV YNLHQKNGFT CMLIGEIFEL MQFLFVVAFT TFLVSCVDY DILFANKMVN HSLHPTEPVK VTLPDAFLPA QVCSARIQEN GSLITILVIA GVFWIHRLIK FIYNICCYWE I HSFYLHAL RIPMSALPYC TWQEVQARIV QTQKEHQICI HKRELTELDI YHRILRFQNY MVALVNKSLL PLRFRLPGLG EA VFFTRGL KYNFELILFW GPGSLFLNEW SLKAEYKRGG QRLELAQRLS NRILWIGIAN FLLCPLILIW QILYAFFSYA EVL KREPGA LGARCWSLYG RCYLRHFNEL EHELQSRLNR GYKPASKYMN CFLSPLLTLL AKNGAFFAGS ILAVLIALTI YDED VLAVE HVLTTVTLLG VTVTVCRSFI PDQHMVFCPE QLLRVILAHI HYMPDHWQGN AHRSQTRDEF AQLFQYKAVF ILEEL LSPI VTPLILIFCL RPRALEIIDF FRNFTVEVVG VGDTCSFAQM DVRQHGHPQW LSAGQTEASV YQQAEDGKTE LSLMHF AIT NPGWQPPRES TAFLGFLKEQ VQRDGAAASL AQGGLLPENA LFTSIQSLQS ESEPLSLIAN VVAGSSCRGP PLPRDLQ GS RHRAEVASAL RSFSPLQPGQ APTGRAHSTM TGSGVDARTA SSGSSVWEGQ LQSLVLSEYA STEMSLHALY MHQLHKQQ A QAEPERHVWH RRESDESGES APDEGGEGAR APQSIPRSAS YPCAAPRPGA PETTALHGGF QRRYGGITDP GTVPRVPSH FSRLPLGGWA EDGQSASRHP EPVPEEGSED ELPPQVHKV

UniProtKB: Autophagy-related protein 9A

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Macromolecule #2: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 2 / Number of copies: 6 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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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: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 646291
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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