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- EMDB-15604: ATG9A and ATG2A form a heteromeric complex essential for autophag... -

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Basic information

Entry
Database: EMDB / ID: EMD-15604
TitleATG9A and ATG2A form a heteromeric complex essential for autophagosome formation
Map data
Sample
  • Complex: Heterotetrameric complex of autophagy related proteins ATG9A and ATG2A
    • Protein or peptide: Autophagy-related protein 9A
    • Protein or peptide: Autophagy-related protein 2 homolog A
KeywordsLipid transfer / lipid scramblase / membrane protein / protein complex / LIPID TRANSPORT
Function / homology
Function and homology information


phagophore / lipid transfer activity / organelle membrane contact site / glycophagy / autophagy of peroxisome / phospholipid scramblase activity / programmed necrotic cell death / positive regulation of autophagosome assembly / protein localization to phagophore assembly site / phagophore assembly site membrane ...phagophore / lipid transfer activity / organelle membrane contact site / glycophagy / autophagy of peroxisome / phospholipid scramblase activity / programmed necrotic cell death / positive regulation of autophagosome assembly / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / bone morphogenesis / phosphatidylinositol-3-phosphate binding / phagophore assembly site / reticulophagy / autophagy of mitochondrion / Macroautophagy / autophagosome assembly / protein-membrane adaptor activity / autophagosome / lipid droplet / PINK1-PRKN Mediated Mitophagy / mitochondrial membrane / trans-Golgi network / recycling endosome / recycling endosome membrane / late endosome / late endosome membrane / endosome / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / membrane
Similarity search - Function
Autophagy-related protein 2/VPS13, C-terminal / Autophagy-related protein 2 / ATG2/VPS13, C terminal domain / Vacuolar protein sorting-associated protein 13-like, N-terminal domain / VPS13-like, N-terminal / Autophagy-related protein 9 / Autophagy protein ATG9
Similarity search - Domain/homology
Autophagy-related protein 2 homolog A / Autophagy-related protein 9A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 32.89 Å
AuthorsChiduza GN / van Vliet AR / De Tito S / Punch EK / Tooze SA
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001187 United Kingdom
European Research Council (ERC)788708European Union
European Molecular Biology Organization (EMBO)325-2017European Union
CitationJournal: Mol Cell / Year: 2022
Title: ATG9A and ATG2A form a heteromeric complex essential for autophagosome formation.
Authors: Alexander R van Vliet / George N Chiduza / Sarah L Maslen / Valerie E Pye / Dhira Joshi / Stefano De Tito / Harold B J Jefferies / Evangelos Christodoulou / Chloë Roustan / Emma Punch / ...Authors: Alexander R van Vliet / George N Chiduza / Sarah L Maslen / Valerie E Pye / Dhira Joshi / Stefano De Tito / Harold B J Jefferies / Evangelos Christodoulou / Chloë Roustan / Emma Punch / Javier H Hervás / Nicola O'Reilly / J Mark Skehel / Peter Cherepanov / Sharon A Tooze /
Abstract: ATG9A and ATG2A are essential core members of the autophagy machinery. ATG9A is a lipid scramblase that allows equilibration of lipids across a membrane bilayer, whereas ATG2A facilitates lipid flow ...ATG9A and ATG2A are essential core members of the autophagy machinery. ATG9A is a lipid scramblase that allows equilibration of lipids across a membrane bilayer, whereas ATG2A facilitates lipid flow between tethered membranes. Although both have been functionally linked during the formation of autophagosomes, the molecular details and consequences of their interaction remain unclear. By combining data from peptide arrays, crosslinking, and hydrogen-deuterium exchange mass spectrometry together with cryoelectron microscopy, we propose a molecular model of the ATG9A-2A complex. Using this integrative structure modeling approach, we identify several interfaces mediating ATG9A-2A interaction that would allow a direct transfer of lipids from ATG2A into the lipid-binding perpendicular branch of ATG9A. Mutational analyses combined with functional activity assays demonstrate their importance for autophagy, thereby shedding light on this protein complex at the heart of autophagy.
History
DepositionAug 18, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15604.png

Downloads & links

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Map

FileDownload / File: emd_15604.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 500 pix.
= 1200. Å		2.4 Å/pix.
x 500 pix.
= 1200. Å		2.4 Å/pix.
x 500 pix.
= 1200. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0192
Minimum - Maximum-0.02069796 - 0.05204869
Average (Standard dev.)0.000008089103 (±0.0013229771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 1200.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15604_msk_1.map
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Half map: #1

Fileemd_15604_half_map_1.map
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Half map: #2

Fileemd_15604_half_map_2.map
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Sample components

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Entire : Heterotetrameric complex of autophagy related proteins ATG9A and ATG2A

EntireName: Heterotetrameric complex of autophagy related proteins ATG9A and ATG2A
Components
  • Complex: Heterotetrameric complex of autophagy related proteins ATG9A and ATG2A
    • Protein or peptide: Autophagy-related protein 9A
    • Protein or peptide: Autophagy-related protein 2 homolog A

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Supramolecule #1: Heterotetrameric complex of autophagy related proteins ATG9A and ATG2A

SupramoleculeName: Heterotetrameric complex of autophagy related proteins ATG9A and ATG2A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
SequenceString: MDYKDDDDKD YKDDDDKDYK DDDDKHHHHH HENLYFQGMA QFDTEYQRLE ASYSDSPPGE EDLLVHVAEG SKSPWHHIEN LDLFFSRVYN LHQKNGFT C MLIGEIFELM QFLFVVAFTT FLVSCVDYDI LFANKMVNHS LHPTEPVKVT LPDAFLPAQ VCSARIQENG ...String:
MDYKDDDDKD YKDDDDKDYK DDDDKHHHHH HENLYFQGMA QFDTEYQRLE ASYSDSPPGE EDLLVHVAEG SKSPWHHIEN LDLFFSRVYN LHQKNGFT C MLIGEIFELM QFLFVVAFTT FLVSCVDYDI LFANKMVNHS LHPTEPVKVT LPDAFLPAQ VCSARIQENG SLITILVIAG VFWIHRLIKF IYNICCYWEI HSFYLHALRI PMSALPYCTW QEVQARIVQ TQKEHQICIH KRELTELDIY HRILRFQNYM VALVNKSLLP LRFRLPGLGE A VFFTRGLK YNFELILFWG PGSLFLNEWS LKAEYKRGGQ RLELAQRLSN RILWIGIANF LL CPLILIW QILYAFFSYA EVLKREPGAL GARCWSLYGR CYLRHFNELE HELQSRLNRG YKP ASKYMN CFLSPLLTLL AKNGAFFAGS ILAVLIALTI YDEDVLAVEH VLTTVTLLGV TVTV CRSFI PDQHMVFCPE QLLRVILAHI HYMPDHWQGN AHRSQTRDEF AQLFQYKAVF ILEEL LSPI VTPLILIFCL RPRALEIIDF FRNFTVEVVG VGDTCSFAQM DVRQHGHPQW LSAGQT EAS VYQQAEDGKT ELSLMHFAIT NPGWQPPRES TAFLGFLKEQ VQRDGAAASL AQGGLLP EN ALFTSIQSLQ SESEPLSLIA NVVAGSSCRG PPLPRDLQGS RHRAEVASAL RSFSPLQP G QAPTGRAHST MTGSGVDART ASSGSSVWEG QLQSLVLSEY ASTEMSLHAL YMHQLHKQQ AQAEPERHVW HRRESDESGE SAPDEGGEGA RAPQSIPRSA SYPCAAPRPG APETTALHGG FQRRYGGIT DPGTVPRVPS HFSRLPLGGW AEDGQSASRH PEPVPEEGSE DELPPQVHKV

UniProtKB: Autophagy-related protein 9A

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Macromolecule #2: Autophagy-related protein 2 homolog A

MacromoleculeName: Autophagy-related protein 2 homolog A / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKD YKDDDDKDYK DDDDKGSGAG AGAGAILNSR VSGLRSRMSR WLWPWSNCVK ERVCRYLLHH YLGHFFQEHL SLDQLSLDLY KGSVALRDIH LEIWSVNEVL ESMESPLELV EGFVGSIEVA VPWAALLTDH CTVRVSGLQL TLQPRRGPAP GAADSQSWAS ...String:
MDYKDDDDKD YKDDDDKDYK DDDDKGSGAG AGAGAILNSR VSGLRSRMSR WLWPWSNCVK ERVCRYLLHH YLGHFFQEHL SLDQLSLDLY KGSVALRDIH LEIWSVNEVL ESMESPLELV EGFVGSIEVA VPWAALLTDH CTVRVSGLQL TLQPRRGPAP GAADSQSWAS CMTTSLQLAQ ECLRDGLPEP SEPPQPLEGL EMFAQTIETV LRRIKVTFLD TVVRVEHSPG DGERGVAVEV RVQRLEYCDE AVRDPSQAPP VDVHQPPAFL HKLLQLAGVR LHYEELPAQE EPPEPPLQIG SCSGYMELMV KLKQNEAFPG PKLEVAGQLG SLHLLLTPRQ LQQLQELLSA VSLTDHEGLA DKLNKSRPLG AEDLWLIEQD LNQQLQAGAV AEPLSPDPLT NPLLNLDNTD LFFSMAGLTS SVASALSELS LSDVDLASSV RSDMASRRLS AQAHPAGKMA PNPLLDTMRP DSLLKMTLGG VTLTLLQTSA PSSGPPDLAT HFFTEFDATK DGPFGSRDFH HLRPRFQRAC PCSHVRLTGT AVQLSWELRT GSRGRRTTSM EVHFGQLEVL ECLWPRGTSE PEYTEILTFP GTLGSQASAR PCAHLRHTQI LRRVPKSRPR RSVACHCHSE LALDLANFQA DVELGALDRL AALLRLATVP AEPPAGLLTE PLPAMEQQTV FRLSAPRATL RLRFPIADLR PEPDPWAGQA VRAEQLRLEL SEPQFRSELS SGPGPPVPTH LELTCSDLHG IYEDGGKPPV PCLRVSKALD PKSTGRKYFL PQVVVTVNPQ SSSTQWEVAP EKGEELELSV ESPCELREPE PSPFSSKRTM YETEEMVIPG DPEEMRTFQS RTLALSRCSL EVILPSVHIF LPSKEVYESI YNRINNDLLM WEPADLLPTP DPAAQPSGFP GPSGFWHDSF KMCKSAFKLA NCFDLTPDSD SDDEDAHFFS VGASGGPQAA APEAPSLHLQ STFSTLVTVL KGRITALCET KDEGGKRLEA VHGELVLDME HGTLFSVSQY CGQPGLGYFC LEAEKATLYH RAAVDDYPLP SHLDLPSFAP PAQLAPTIYP SEEGVTERGA SGRKGQGRGP HMLSTAVRIH LDPHKNVKEF LVTLRLHKAT LRHYMALPEQ SWHSQLLEFL DVLDDPVLGY LPPTVITILH THLFSCSVDY RPLYLPVRVL ITAETFTLSS NIIMDTSTFL LRFILDDSAL YLSDKCEVET LDLRRDYVCV LDVDLLELVI KTWKGSTEGK LSQPLFELRC SNNVVHVHSC ADSCALLVNL LQYVMSTGDL HPPPRPPSPT EIAGQKLSES PASLPSCPPV ETALINQRDL ADALLDTERS LRELAQPSGG HLPQASPISV YLFPGERSGA PPPSPPVGGP AGSLGSCSEE KEDEREEEGD GDTLDSDEFC ILDAPGLGIP PRDGEPVVTQ LHPGPIVVRD GYFSRPIGST DLLRAPAHFP VPSTRVVLRE VSLVWHLYGG RDFGPHPGHR ARTGLSGPRS SPSRCSGPNR PQNSWRTQGG SGRQHHVLME IQLSKVSFQH EVYPAEPATG PAAPSQELEE RPLSRQVFIV QELEVRDRLA SSQINKFLYL HTSERMPRRA HSNMLTIKAL HVAPTTNLGG PECCLRVSLM PLRLNVDQDA LFFLKDFFTS LVAGINPVVP GETSAEARPE TRAQPSSPLE GQAEGVETTG SQEAPGGGHS PSPPDQQPIY FREFRFTSEV PIWLDYHGKH VTMDQVGTFA GLLIGLAQLN CSELKLKRLC CRHGLLGVDK VLGYALNEWL QDIRKNQLPG LLGGVGPMHS VVQLFQGFRD LLWLPIEQYR KDGRLMRGLQ RGAASFGSST ASAALELSNR LVQAIQATAE TVYDILSPAA PVSRSLQDKR SARRLRRGQQ PADLREGVAK AYDTVREGIL DTAQTICDVA SRGHEQKGLT GAVGGVIRQL PPTVVKPLIL ATEATSSLLG GMRNQIVPDA HKDHALKWRS DSAQDNSAVD GTAGPGSTGS R

UniProtKB: Autophagy-related protein 2 homolog A

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.025 mg/mL
BufferpH: 8 / Details: 50 mM HEPES, 250 mM NaCl, 1 mM TCEP
StainingType: NEGATIVE / Material: Uranyl Acetate
GridModel: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
DetailsComplex was reconstituted and subjected to size exclusion before grid prep.

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: OTHER / Number grids imaged: 1 / Number real images: 1847 / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 88107
Startup modelType of model: INSILICO MODEL
In silico model: Generated using stochastic gradient descent in RELION 3.1
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 32.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 2058
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: Done using RELION 3.1
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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