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- PDB-9tw3: Cryo-EM structure of human VPS34-CI in complex with GABARAP - alt... -

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Basic information

Entry
Database: PDB / ID: 9tw3
TitleCryo-EM structure of human VPS34-CI in complex with GABARAP - alternative conformation
Components
  • Beclin 1-associated autophagy-related key regulator
  • Beclin-1
  • Gamma-aminobutyric acid receptor-associated protein
  • Nuclear receptor-binding factor 2
  • Phosphatidylinositol 3-kinase catalytic subunit type 3
  • Phosphoinositide 3-kinase regulatory subunit 4
KeywordsLIPID BINDING PROTEIN / Lipid kinase / Complex / Autophagy
Function / homology
Function and homology information


extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / extrinsic component of phagophore assembly site membrane / nucleus-vacuole junction / cellular response to aluminum ion / positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / positive regulation of protein K48-linked ubiquitination / Synthesis of PIPs at the late endosome membrane ...extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / extrinsic component of phagophore assembly site membrane / nucleus-vacuole junction / cellular response to aluminum ion / positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / positive regulation of protein K48-linked ubiquitination / Synthesis of PIPs at the late endosome membrane / cellular response to oxygen-glucose deprivation / Synthesis of PIPs at the early endosome membrane / positive regulation of stress granule assembly / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / presynaptic endosome / regulation of Rac protein signal transduction / phosphatidylinositol 3-kinase complex, class III / positive regulation of attachment of mitotic spindle microtubules to kinetochore / host-mediated activation of viral genome replication / engulfment of apoptotic cell / negative regulation of lysosome organization / regulation of protein complex stability / phosphatidylinositol kinase activity / SMAD protein signal transduction / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol 3-kinase regulator activity / phagophore assembly site membrane / early endosome to late endosome transport / receptor catabolic process / cytoplasmic side of mitochondrial outer membrane / response to L-leucine / protein targeting to vacuole / protein targeting to lysosome / mitochondria-associated endoplasmic reticulum membrane contact site / late endosome to vacuole transport / positive regulation of lysosome organization / endosome organization / GABA receptor binding / Dengue virus modulates apoptosis / positive regulation of natural killer cell mediated cytotoxicity / phosphatidylethanolamine binding / pexophagy / positive regulation of autophagosome assembly / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / reticulophagy / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / extrinsic apoptotic signaling pathway via death domain receptors / 1-phosphatidylinositol-3-kinase activity / post-transcriptional regulation of gene expression / response to vitamin E / Macroautophagy / endosome to lysosome transport / p38MAPK cascade / autophagosome membrane docking / RSV-host interactions / response to iron(II) ion / cytoplasmic pattern recognition receptor signaling pathway / phosphatidylinositol phosphate biosynthetic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of protein phosphorylation / phosphatidylinositol-mediated signaling / smooth endoplasmic reticulum / protein-membrane adaptor activity / autolysosome / autophagosome membrane / positive regulation of intrinsic apoptotic signaling pathway / PI3K Cascade / autophagosome maturation / RHO GTPases Activate NADPH Oxidases / JNK cascade / mitotic metaphase chromosome alignment / autophagosome assembly / axoneme / protein targeting / mitophagy / negative regulation of programmed cell death / synaptic vesicle endocytosis / cellular defense response / cellular response to glucose starvation / phosphatidylinositol 3-kinase binding / beta-tubulin binding / regulation of macroautophagy / phagocytic vesicle / positive regulation of autophagy / response to endoplasmic reticulum stress / negative regulation of TORC1 signaling / sperm midpiece / cellular response to epidermal growth factor stimulus / autophagosome / cellular response to copper ion / cellular response to amino acid starvation / cellular response to starvation / phosphatidylinositol 3-kinase/protein kinase B signal transduction
Similarity search - Function
Nuclear receptor-binding factor 2, C-terminal / Nuclear receptor-binding factor 2, MIT domain / Nuclear receptor-binding factor 2 / Nuclear receptor-binding factor 2, autophagy regulator / MIT domain of nuclear receptor-binding factor 2 / UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting ...Nuclear receptor-binding factor 2, C-terminal / Nuclear receptor-binding factor 2, MIT domain / Nuclear receptor-binding factor 2 / Nuclear receptor-binding factor 2, autophagy regulator / MIT domain of nuclear receptor-binding factor 2 / UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Phosphatidylinositol 3-kinase, Vps34 type / : / : / PIK3R4-like, middle domain / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / HEAT, type 2 / HEAT repeat profile. / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / Armadillo-like helical / WD domain, G-beta repeat / Armadillo-type fold / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / Serine/Threonine protein kinases, catalytic domain / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / MYRISTIC ACID / Gamma-aminobutyric acid receptor-associated protein / Beclin-1 / Beclin 1-associated autophagy-related key regulator / Phosphatidylinositol 3-kinase catalytic subunit type 3 / Nuclear receptor-binding factor 2 / Phosphoinositide 3-kinase regulatory subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDessus, A.N. / Williams, R.L.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105184308 United Kingdom
Cancer Research UKDRCPGM 100014 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: A GABARAP-PtdIns3K-C1 positive feedback loop at the heart of the phagophore nucleation.
Authors: Antoine N Dessus / Yohei Ohashi / Maxime Bourguet / Tomos E Morgan / Anastasia Nunez / Maria Manifava / Nicholas T Ktistakis / Roger L Williams /
Abstract: In mammalian cells, autophagosomes can reach diameters of over 1000 nm within 30 min after triggering starvation, but how such substantial amounts of membranes can be synthesized remains elusive. ...In mammalian cells, autophagosomes can reach diameters of over 1000 nm within 30 min after triggering starvation, but how such substantial amounts of membranes can be synthesized remains elusive. The phagophore initiation needs the lipid kinase PIK3C3-Complex 1 (PtdIns3K-C1), which produces phosphatidylinositol-3-phosphate (PtdIns3P). PtdIns3P recruits WIPI2 that facilitates lipidation of mammalian ATG8 (mATG8) family proteins on phagophores. Here we show that recombinant membrane-coupled GABARAP binds to and potently activates PtdIns3K-C1. By a combination of cryo-electron microscopy, structural mass spectrometry, activity assays and mutagenesis, we show that GABARAP activates PtdIns3K-C1 through two binding sites. We propose that once GABARAP is indirectly recruited by PtdIns3P generated by basal activity of PtdIns3K-C1, a positive feedback loop is formed where PtdIns3K-C1 interacts with GABARAP and becomes activated to produce more PtdIns3P, thereby further stimulating GABARAP lipidation. This mechanism would be central for autophagosome biogenesis, where enlarged membranes need to be rapidly synthesized.
History
DepositionJan 13, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
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Revision 1.2Sep 16, 2026Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 3-kinase catalytic subunit type 3
B: Phosphoinositide 3-kinase regulatory subunit 4
C: Beclin-1
D: Beclin 1-associated autophagy-related key regulator
E: Nuclear receptor-binding factor 2
F: Gamma-aminobutyric acid receptor-associated protein
G: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)440,49212
Polymers439,6667
Non-polymers8275
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 6 types, 7 molecules ABCGDEF

#1: Protein Phosphatidylinositol 3-kinase catalytic subunit type 3 / PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase ...PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase class 3 / hVps34


Mass: 101680.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C3, VPS34 / Production host: Homo sapiens (human) / References: UniProt: Q8NEB9, phosphatidylinositol 3-kinase
#2: Protein Phosphoinositide 3-kinase regulatory subunit 4 / PI3-kinase regulatory subunit 4 / PI3-kinase p150 subunit / Phosphoinositide 3-kinase adaptor protein


Mass: 154790.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal tag / Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R4, VPS15 / Production host: Homo sapiens (human)
References: UniProt: Q99570, non-specific serine/threonine protein kinase
#3: Protein Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 51953.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BECN1, GT197 / Production host: Homo sapiens (human) / References: UniProt: Q14457
#4: Protein Beclin 1-associated autophagy-related key regulator / Barkor / Autophagy-related protein 14-like protein / Atg14L


Mass: 55461.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Insertion of a Threonine in position 2. / Source: (gene. exp.) Homo sapiens (human) / Gene: ATG14, ATG14L, KIAA0831 / Production host: Homo sapiens (human) / References: UniProt: Q6ZNE5
#5: Protein Nuclear receptor-binding factor 2 / NRBF-2 / Comodulator of PPAR and RXR


Mass: 9716.190 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MIT domain of NRBF2 (1-84) / Source: (gene. exp.) Homo sapiens (human) / Gene: NRBF2, COPR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96F24
#6: Protein Gamma-aminobutyric acid receptor-associated protein / GABA(A) receptor-associated protein / MM46


Mass: 14111.165 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal tag and deletion of L117. / Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, FLC3B, HT004 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O95166

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Non-polymers , 4 types, 5 molecules

#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Protein complex of VPS34-CI, NRBF2 MIT and GABARAPCOMPLEX#1-#60RECOMBINANT
2Human VPS34-CICOMPLEX#1-#41RECOMBINANT
3NRBF2 MIT domainCOMPLEX#51RECOMBINANT
4GABARAPCOMPLEX#61RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.387212 MDaNO
210.363427 MDaNO
310.09699 MDaNO
410.14086 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDPlasmid
21Homo sapiens (human)9606
32Homo sapiens (human)9606pCAG
43Escherichia coli BL21(DE3) (bacteria)469008
54Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESHEPES1
2100 mMsodium chlorideNaCl1
31 mMTris-(2-Carboxyethyl)phosphineTCEP1
44 mMCHAPSOCHAPSO1
50.005 % (v/v)Nonidet P-40Nonidet-P-401
SpecimenConc.: 1.92 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 3.6 uM VPS34-CI was mixed with 3.6 uM NRBF2 MIT and 40 uM GABARAP.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 287.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.97 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 18226
Image scansWidth: 4092 / Height: 5760

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Processing

EM software
IDNameVersionCategoryImage processing-ID
1crYOLO1.7.5particle selection1
2EPUimage acquisition
4cryoSPARC4.6.2CTF correction1
7UCSF ChimeraX1.7.1model fitting
8ISOLDE1.7.1model fitting
10TEMPy1.2.0model refinement
11PHENIX1.21.2_5419model refinement
12cryoSPARC4.6.2initial Euler assignment1
13cryoSPARC4.6.2final Euler assignment1
14cryoSPARC4.6.2classification1
15cryoSPARC4.6.23D reconstruction1
16crYOLO1.7.5particle selection2
17cryoSPARC4.6.2CTF correction2
18cryoSPARC4.6.2initial Euler assignment2
19cryoSPARC4.6.2final Euler assignment2
20cryoSPARC4.6.2classification2
21cryoSPARC4.6.23D reconstruction2
Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
IDImage processing-IDNum. of particles selected
11973900
22973900
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.6FSC 0.5 CUT-OFF57783819TW3POINT
23.6FSC 0.5 CUT-OFF57783819TW3POINT
33.6FSC 0.5 CUT-OFF57783829TW3POINT
43.6FSC 0.5 CUT-OFF57783829TW3POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00323606
ELECTRON MICROSCOPYf_angle_d0.62631884
ELECTRON MICROSCOPYf_dihedral_angle_d6.6153138
ELECTRON MICROSCOPYf_chiral_restr0.0443522
ELECTRON MICROSCOPYf_plane_restr0.0064094

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