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Structure paper

TitleA novel RAB5 binding site in human VPS34-CII that is likely the primordial site in eukaryotic evolution
Journal, issue, pagesElife, Year 2026
Publish dateJul 9, 2025 (structure data deposition date)
AuthorsSpokaite S / Ohashi Y / Bourguet M / Dessus AN / Williams RL
External linksElife / Search PubMed
MethodsEM (single particle) / EM (subtomogram averaging)
Resolution3.15 - 9.88 Å
Structure data

EMDB-54312: VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L, focused refinement on the adaptor arm)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-54313: VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L, focused refinement on the kinase arm)
Method: EM (single particle) / Resolution: 3.15 Å

EMDB-54314: VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L), focused refinement on the base of the complex
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-54315: VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L, focused refinement on the interface between RAB5A and VPS34)
Method: EM (single particle) / Resolution: 3.25 Å

EMDB-54316: VPS34-CII (VPS34 199-REIE-202 > 199-AAAA-202 mutant) bound to RAB5A-GTP (Q79L), consensus refinement
Method: EM (single particle) / Resolution: 3.43 Å

EMDB-54317: VPS34-CII (VPS34 199-REIE-202 > 199-AAAA-202 mutant) bound to RAB5A-GTP (Q79L); unsharpened composite map
Method: EM (single particle) / Resolution: 3.15 Å

EMDB-54318: VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit, focused refinement on the kinase arm
Method: EM (single particle) / Resolution: 3.55 Å

EMDB-54319: VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit, focused refinement on the adaptor arm
Method: EM (single particle) / Resolution: 4.09 Å

EMDB-54320: VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit, focused refinement of the RAB5A interface with VPS15
Method: EM (single particle) / Resolution: 3.52 Å

EMDB-54321: VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit, consensus refinement
Method: EM (single particle) / Resolution: 3.68 Å

EMDB-54322: VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit; unsharpened composite map
Method: EM (single particle) / Resolution: 3.52 Å

54358

9rx5

EMDB-54358: VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L), primary composite map processed with CryoTEN
PDB-9rx5: VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L)
Method: EM (single particle) / Resolution: 3.15 Å

54359

9rx6

EMDB-54359: VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit, composite map processed with CryoTEN.
PDB-9rx6: VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit
Method: EM (single particle) / Resolution: 3.52 Å

54361

9rx8

EMDB-54361: Apo VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG), consensus refinement map processed with CryoTEN
PDB-9rx8: Apo VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG)
Method: EM (single particle) / Resolution: 3.87 Å

54362

9rx9

EMDB-54362: VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS34 subunit, primary map processed with CryoTEN
PDB-9rx9: VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS34 subunit
Method: EM (single particle) / Resolution: 3.99 Å

54363

9rxa

EMDB-54363: VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS15 subunit, primary map processed with CryoTEN
PDB-9rxa: VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS15 subunit
Method: EM (single particle) / Resolution: 4.0 Å

54364

9rxb

EMDB-54364: VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) bound to RAB5A (Q79L) on the VPS34 and VPS15 subunits, primary map processed with CryoTEN
PDB-9rxb: VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) bound to RAB5A (Q79L) on the VPS34 and VPS15 subunits
Method: EM (single particle) / Resolution: 4.03 Å

54560

9s47

EMDB-54560, PDB-9s47:
Human complex II-BATS bound to membrane-attached Rab5a-GTP
Method: EM (subtomogram averaging) / Resolution: 9.88 Å

Chemicals

ChemComp-MYR:
MYRISTIC ACID

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

Source
  • homo sapiens (human)
KeywordsENDOCYTOSIS / Lipid kinase / GTPase / kinase / autophagy / endocytic trafficking / SIGNALING PROTEIN / endocytic sorting / endosome maturation

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