6DJQ | pdb_00006djq

Vps1 GTPase-BSE fusion complexed with GDP.AlF4-

• PDB DOI: https://doi.org/10.2210/pdb6DJQ/pdb

• Classification: HYDROLASE
• Organism(s): Thermochaetoides thermophila DSM 1495
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-05-25 Released: 2018-08-22 
• Deposition Author(s): Varlakhanova, N.V., Brady, T.M., Tornabene, B.A., Hosford, C.J., Chappie, J.S., Ford, M.G.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.279 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Structures of the fungal dynamin-related protein Vps1 reveal a unique, open helical architecture.

Varlakhanova, N.V., Alvarez, F.J.D., Brady, T.M., Tornabene, B.A., Hosford, C.J., Chappie, J.S., Zhang, P., Ford, M.G.J.

(2018) J Cell Biol 217: 3608-3624

• PubMed: 30087125 
• DOI: https://doi.org/10.1083/jcb.201712021
• Primary Citation Related Structures: 
  6DEF, 6DI7, 6DJQ


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 
• Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA.
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA.
Department of Molecular Medicine, Cornell University, Ithaca, NY.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 174.38 kDa 
• Atom Count: 10,085 
• Modeled Residue Count: 1,340 
• Deposited Residue Count: 1,564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vps1 GTPase-BSE	A, B, C, D	391	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  Gene Names: CTHT_0061810
UniProt
Find proteins for G0SFF0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SFF0  Go to UniProtKB:  G0SFF0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	E [auth A], I [auth B], M [auth C], Q [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ALF	F [auth A], J [auth B], N [auth C], R [auth D]	TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG	G [auth A], K [auth B], O [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	H [auth A], L [auth B], P [auth C], T [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.279 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.06	α = 90
b = 121.22	β = 90.6
c = 104.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Varlakhanova, N.V., Brady, T.M., Tornabene, B.A., Hosford, C.J., Chappie, J.S., Ford, M.G.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM120102

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2018-10-17
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description