9TW3 | pdb_00009tw3

Cryo-EM structure of human VPS34-CI in complex with GABARAP - alternative conformation

PDB DOI: https://doi.org/10.2210/pdb9TW3/pdb
EM Map EMD-56358: EMDB EMDataResource

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-01-13 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: 3.60 Å
Resolution: 3.60 Å
Resolution: 3.60 Å
Resolution: 3.60 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 1.1 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

DOI: https://doi.org/10.1038/s41467-026-76135-w

Macromolecule Content

Total Structure Weight: 440.49 kDa
Atom Count: 23,420
Modeled Residue Count: 2,897
Deposited Residue Count: 3,854
Unique protein chains: 6

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
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
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, G	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
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
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
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

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor-associated protein	F	119	Homo sapiens	Mutation(s): 0 Gene Names: GABARAP, FLC3B, HT004
UniProt & NIH Common Fund Data Resources
Find proteins for O95166 (Homo sapiens) Explore O95166 Go to UniProtKB: O95166
GTEx: ENSG00000170296
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
MYR (Subject of Investigation/LOI) Query on MYR Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D]	K [auth D], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain K [auth D] Focus chain L [auth D]
MG (Subject of Investigation/LOI) Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]