9BL8 | pdb_00009bl8

MIT (L7C/A43C) Domain of Vps4p

• PDB DOI: https://doi.org/10.2210/pdb9BL8/pdb

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


• Deposited: 2024-04-29 Released: 2025-03-12 
• Deposition Author(s): Wienkers, H.J., Han, H., Whitby, F.G., Hill, C.P.
• 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: 1.30 Å
• R-Value Free: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

Literature

Vps4 substrate binding and coupled mechanisms of Vps4p substrate recruitment and release from autoinhibition.

Wienkers, H.J., Han, H., Whitby, F.G., Hill, C.P.

(2024) bioRxiv 

• PubMed: 39282404 
• DOI: https://doi.org/10.1101/2024.09.07.611824
• Primary Citation of Related Structures:  
  9BL8


• PubMed Abstract: 
  

  The ESCRT pathway's AAA+ ATPase, Vps4p, remodels ESCRT-III complexes to drive membrane fission. Here, we use peptide binding assays to further the understanding of substrate specificity and the mechanism of autoinhibition. Our results reveal unexpected sequence preference to the substrate binding groove and an elegant mechanism of regulation that couples localization to substrate with release from autoinhibition.

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Organizational Affiliation: 
• Department of Biochemistry, University of Utah, Salt Lake City, Utah, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.56 kDa 
• Atom Count: 869 
• Modeled Residue Count: 83 
• Deposited Residue Count: 83 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 4	A	83	Saccharomyces cerevisiae	Mutation(s): 2  Gene Names: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10
UniProt
Find proteins for P52917 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P52917  Go to UniProtKB:  P52917

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 20.699	α = 90
b = 42.939	β = 90
c = 96.463	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Wienkers, H.J., Han, H., Whitby, F.G., Hill, C.P.

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

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release