7BL1

human complex II-BATS bound to membrane-attached Rab5a-GTP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.80 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes.

Tremel, S.Ohashi, Y.Morado, D.R.Bertram, J.Perisic, O.Brandt, L.T.L.von Wrisberg, M.K.Chen, Z.A.Maslen, S.L.Kovtun, O.Skehel, M.Rappsilber, J.Lang, K.Munro, S.Briggs, J.A.G.Williams, R.L.

(2021) Nat Commun 12: 1564-1564

  • DOI: 10.1038/s41467-021-21695-2
  • Primary Citation of Related Structures:  
    7BL1

  • PubMed Abstract: 
  • The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal and spatial control. PI3P is generated by two complexes that both contain the lipid kinase VPS34: complex II on endosomes (VPS34/VPS15/Beclin 1/UVRAG), and complex I on autophagosomes (VPS34/VPS15/Beclin 1/ATG14L) ...

    The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal and spatial control. PI3P is generated by two complexes that both contain the lipid kinase VPS34: complex II on endosomes (VPS34/VPS15/Beclin 1/UVRAG), and complex I on autophagosomes (VPS34/VPS15/Beclin 1/ATG14L). The endosomal GTPase Rab5 binds complex II, but the mechanism of VPS34 activation by Rab5 has remained elusive, and no GTPase is known to bind complex I. Here we show that Rab5a-GTP recruits endocytic complex II to membranes and activates it by binding between the VPS34 C2 and VPS15 WD40 domains. Electron cryotomography of complex II on Rab5a-decorated vesicles shows that the VPS34 kinase domain is released from inhibition by VPS15 and hovers over the lipid bilayer, poised for catalysis. We also show that the GTPase Rab1a, which is known to be involved in autophagy, recruits and activates the autophagy-specific complex I, but not complex II. Both Rabs bind to the same VPS34 interface but in a manner unique for each. These findings reveal how VPS34 complexes are activated on membranes by specific Rab GTPases and how they are recruited to unique cellular locations.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK. rlw@mrc-lmb.cam.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UV radiation resistance-associated gene protein AAA699Homo sapiensMutation(s): 0 
Gene Names: UVRAG
Find proteins for Q9P2Y5 (Homo sapiens)
Explore Q9P2Y5 
Go to UniProtKB:  Q9P2Y5
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PHAROS:  Q9P2Y5
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase catalytic subunit type 3 BBB887Homo sapiensMutation(s): 0 
Gene Names: PIK3C3VPS34
EC: 2.7.1.137
Find proteins for Q8NEB9 (Homo sapiens)
Explore Q8NEB9 
Go to UniProtKB:  Q8NEB9
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PHAROS:  Q8NEB9
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoinositide 3-kinase regulatory subunit 4 CCC1371Homo sapiensMutation(s): 0 
Gene Names: PIK3R4VPS15
EC: 2.7.11.1
Find proteins for Q99570 (Homo sapiens)
Explore Q99570 
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PHAROS:  Q99570
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Beclin-1 EEE450Homo sapiensMutation(s): 0 
Gene Names: BECN1GT197
Find proteins for Q14457 (Homo sapiens)
Explore Q14457 
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PHAROS:  Q14457
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
unknown peptide FFF22Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-5A DDD168Homo sapiensMutation(s): 0 
Gene Names: RAB5ARAB5
EC: 3.6.5.2
Find proteins for P20339 (Homo sapiens)
Explore P20339 
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PHAROS:  P20339
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
DDD
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
DDD
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.80 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105184308
Medical Research Council (MRC, United Kingdom)United KingdomMC_U10517878
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/16
Cancer Research UKC14801/A21211
European Research Council (ERC)United KingdomERC-CoG-648432 MEMBRANEFUSION
Wellcome TrustUnited KingdomNo. 103139
Wellcome TrustUnited KingdomNo. 203149

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references