9RX6 | pdb_00009rx6

VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit

PDB DOI: https://doi.org/10.2210/pdb9RX6/pdb
EM Map EMD-54359: EMDB EMDataResource

Classification: ENDOCYTOSIS
Organism(s): Homo sapiens
Expression System: Homo sapiens, Escherichia coli
Mutation(s): Yes

Deposited: 2025-07-10 Released: 2026-06-03
Deposition Author(s): Spokaite, S., Ohashi, Y., Dessus, A.N., Bourguet, M., Williams, R.L.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Cancer Research UK

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.52 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A novel RAB5 binding site in human VPS34-CII that is likely the primordial site in eukaryotic evolution

Spokaite, S., Ohashi, Y., Bourguet, M., Dessus, A.N., Williams, R.L.

(2026) Elife

DOI: https://doi.org/10.7554/eLife.110040.3

Macromolecule Content

Total Structure Weight: 411.25 kDa
Atom Count: 24,058
Modeled Residue Count: 2,977
Deposited Residue Count: 3,618
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): 3 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	1,370	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	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
UV radiation resistance associated protein	D	699	Homo sapiens	Mutation(s): 0 Gene Names: UVRAG
UniProt
Find proteins for Q6P1X0 (Homo sapiens) Explore Q6P1X0 Go to UniProtKB: Q6P1X0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6P1X0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-5A	E [auth F]	212	Homo sapiens	Mutation(s): 3 Gene Names: RAB5A, RAB5 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P20339 (Homo sapiens) Explore P20339 Go to UniProtKB: P20339
PHAROS: P20339 GTEx: ENSG00000144566
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20339
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download:Ideal Coordinates CCD File SDF format, chain K [auth F] MOL2 format, chain K [auth F] mmCIF format, chain K [auth F]	K [auth F]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain K [auth F] Interactions & Density Focus chain K [auth F]
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
MYR (Subject of Investigation/LOI) Query on MYR Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth F] MOL2 format, chain H [auth B] MOL2 format, chain J [auth F] mmCIF format, chain H [auth B] mmCIF format, chain J [auth F]	H [auth B], J [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain J [auth F] Interactions & Density Focus chain H [auth B] Focus chain J [auth F]