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Structure paper

TitleStructures of the fungal dynamin-related protein Vps1 reveal a unique, open helical architecture.
Journal, issue, pagesJ Cell Biol, Vol. 217, Issue 10, Page 3608-3624, Year 2018
Publish dateOct 1, 2018
AuthorsNatalia V Varlakhanova / Frances J D Alvarez / Tyler M Brady / Bryan A Tornabene / Christopher J Hosford / Joshua S Chappie / Peijun Zhang / Marijn G J Ford /
PubMed AbstractDynamin-related proteins (DRPs) are large multidomain GTPases required for diverse membrane-remodeling events. DRPs self-assemble into helical structures, but how these structures are tailored to ...Dynamin-related proteins (DRPs) are large multidomain GTPases required for diverse membrane-remodeling events. DRPs self-assemble into helical structures, but how these structures are tailored to their cellular targets remains unclear. We demonstrate that the fungal DRP Vps1 primarily localizes to and functions at the endosomal compartment. We present crystal structures of a Vps1 GTPase-bundle signaling element (BSE) fusion in different nucleotide states to capture GTP hydrolysis intermediates and concomitant conformational changes. Using cryoEM, we determined the structure of full-length GMPPCP-bound Vps1. The Vps1 helix is more open and flexible than that of dynamin. This is due to further opening of the BSEs away from the GTPase domains. A novel interface between adjacent GTPase domains forms in Vps1 instead of the contacts between the BSE and adjacent stalks and GTPase domains as seen in dynamin. Disruption of this interface abolishes Vps1 function in vivo. Hence, Vps1 exhibits a unique helical architecture, highlighting structural flexibilities of DRP self-assembly.
External linksJ Cell Biol / PubMed:30087125 / PubMed Central
MethodsEM (helical sym.) / X-ray diffraction
Resolution2.26 - 11.0 Å
Structure data

EMDB-7874:
Helical assembly of the fungal dynamin-related Vps1 in the presence of GMPPCP
Method: EM (helical sym.) / Resolution: 11.0 Å

PDB-6def:
Vps1 GTPase-BSE fusion complexed with GMPPCP
Method: X-RAY DIFFRACTION / Resolution: 2.26 Å

PDB-6di7:
Vps1 GTPase-BSE fusion complexed with GDP
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-6djq:
Vps1 GTPase-BSE fusion complexed with GDP.AlF4-
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

Chemicals

ChemComp-GCP:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

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

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

ChemComp-NA:
Unknown entry

Source
  • chaetomium thermophilum (fungus)
KeywordsHYDROLASE / Vps1 / Vacuolar Protein Sorting 1 / Dynamin-Related Protein / DRP / GTPase / GMPPCP / Endosome / Vacuole / GDP / dynamin / GDP.AlF4- / transition state

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