9TZ3 | pdb_00009tz3

Cryo-EM structure of human VPS34-CI with ADP:MgF3

PDB DOI: https://doi.org/10.2210/pdb9TZ3/pdb
EM Map EMD-56458: EMDB EMDataResource

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2026-01-22 Released: 2026-08-05
Deposition Author(s): Dessus, A.N., Williams, R.L.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Cancer Research UK

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Resolution: 3.66 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A GABARAP-PtdIns3K-C1 positive feedback loop at the heart of the phagophore nucleation.

Dessus, A.N., Ohashi, Y., Bourguet, M., Morgan, T.E., Nunez, A., Manifava, M., Ktistakis, N.T., Williams, R.L.

(2026) Nat Commun 17

PubMed: 42693081 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-026-76135-w
Primary Citation Related Structures:
9TW2, 9TW3, 9TZ3

PubMed 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. 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.

Organizational Affiliation

MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.

Macromolecule Content

Total Structure Weight: 426.83 kDa
Atom Count: 22,318
Modeled Residue Count: 2,760
Deposited Residue Count: 3,735
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase catalytic subunit type 3	A	887	Homo sapiens	Mutation(s): 0 Gene Names: PIK3C3, VPS34 EC: 2.7.1.137
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEB9 (Homo sapiens) Explore Q8NEB9 Go to UniProtKB: Q8NEB9
PHAROS: Q8NEB9 GTEx: ENSG00000078142
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NEB9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoinositide 3-kinase regulatory subunit 4	B	1,371	Homo sapiens	Mutation(s): 0 Gene Names: PIK3R4, VPS15 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99570 (Homo sapiens) Explore Q99570 Go to UniProtKB: Q99570
PHAROS: Q99570 GTEx: ENSG00000196455
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99570
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beclin-1	C, F	450	Homo sapiens	Mutation(s): 0 Gene Names: BECN1, GT197
UniProt & NIH Common Fund Data Resources
Find proteins for Q14457 (Homo sapiens) Explore Q14457 Go to UniProtKB: Q14457
PHAROS: Q14457 GTEx: ENSG00000126581
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14457
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beclin 1-associated autophagy-related key regulator	D	493	Homo sapiens	Mutation(s): 0 Gene Names: ATG14, ATG14L, KIAA0831
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZNE5 (Homo sapiens) Explore Q6ZNE5 Go to UniProtKB: Q6ZNE5
PHAROS: Q6ZNE5 GTEx: ENSG00000126775
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6ZNE5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor-binding factor 2	E	84	Homo sapiens	Mutation(s): 0 Gene Names: NRBF2, COPR
UniProt & NIH Common Fund Data Resources
Find proteins for Q96F24 (Homo sapiens) Explore Q96F24 Go to UniProtKB: Q96F24
PHAROS: Q96F24 GTEx: ENSG00000148572
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96F24
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MYR (Subject of Investigation/LOI) Query on MYR Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth F] SDF format, chain L [auth C] MOL2 format, chain M [auth F] MOL2 format, chain L [auth C] mmCIF format, chain M [auth F] mmCIF format, chain L [auth C]	L [auth C], M [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain M [auth F] Interactions & Density Focus chain L [auth C] Focus chain M [auth F]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]