Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 39.10 kDa 
• Atom Count: 2074 
• Residue Count: 288 
• Unique protein chains: 1

2QP9

Crystal Structure of S.cerevisiae Vps4

• DOI: 10.2210/pdb2QP9/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-07-23 Released: 2007-10-09 
• Deposition Author(s): Xiao, J., Xu, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.288 
• R-Value Work: 0.258 
• R-Value Observed: 0.260 

Literature

Structural characterization of the ATPase reaction cycle of endosomal AAA protein Vps4.

Xiao, J., Xia, H., Yoshino-Koh, K., Zhou, J., Xu, Z.

(2007) J Mol Biol 374: 655-670

• PubMed: 17949747 
• DOI: 10.1016/j.jmb.2007.09.067
• Primary Citation of Related Structures:  
  2QPA, 2QP9


• PubMed Abstract: 
  

The multivesicular body (MVB) pathway functions in multiple cellular processes including cell surface receptor down-regulation and viral budding from host cells. An important step in the MVB pathway is the correct sorting of cargo molecules, which requires the assembly and disassembly of endosomal sorting complexes required for transport (ESCRTs) on the endosomal membrane. Disassembly of the ESCRTs is catalyzed by ATPase associated with various cellular activities (AAA) protein Vps4. Vps4 contains a single AAA domain and undergoes ATP-dependent quaternary structural change to disassemble the ESCRTs. Structural and biochemical analyses of the Vps4 ATPase reaction cycle are reported here. Crystal structures of Saccharomyces cerevisiae Vps4 in both the nucleotide-free form and the ADP-bound form provide the first structural view illustrating how nucleotide binding might induce conformational changes within Vps4 that lead to oligomerization and binding to its substrate ESCRT-III subunits. In contrast to previous models, characterization of the Vps4 structure now supports a model where the ground state of Vps4 in the ATPase reaction cycle is predominantly a monomer and the activated state is a dodecamer. Comparison with a previously reported human VPS4B structure suggests that Vps4 functions in the MVB pathway via a highly conserved mechanism supported by similar protein-protein interactions during its ATPase reaction cycle.

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Organizational Affiliation: 

Life Sciences Institute and Department of Biological Chemistry, Medical School, University of Michigan, Ann Arbor, MI 48109, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 4	X	355	Saccharomyces cerevisiae	Mutation(s): 3  Gene Names: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10
Find proteins for P52917 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P52917  Go to UniProtKB:  P52917

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	X	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	X	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.288 
• R-Value Work: 0.258 
• R-Value Observed: 0.260 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.553	α = 90
b = 86.553	β = 90
c = 236.061	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-07-23 
• Released Date: 2007-10-09 
Deposition Author(s): Xiao, J., Xu, Z.

Revision History 

• Version 1.0: 2007-10-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description