7X4O

Crystal structure of Vps17p PX from S. cerevisiae (Space)

• PDB DOI: https://doi.org/10.2210/pdb7X4O/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-03 Released: 2022-05-18 
• Deposition Author(s): Maita, N., Kohda, D., Obita, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of the PX domain of Vps17p from Saccharomyces cerevisiae.

Obita, T., Inaka, K., Kohda, D., Maita, N.

(2022) Acta Crystallogr F Struct Biol Commun 78: 210-216

• PubMed: 35506766 
• DOI: https://doi.org/10.1107/S2053230X22004472
• Primary Citation of Related Structures:  
  7X4O


• PubMed Abstract: 
  

  The structure determination of the PX (phox homology) domain of the Saccharomyces cerevisiae Vps17p protein presented a challenging case for molecular replacement because it has noncrystallographic symmetry close to a crystallographic axis. The combination of diffraction-quality crystals grown under microgravity on the International Space Station and a highly accurate template structure predicted by AlphaFold2 provided the key to successful crystal structure determination. Although the structure of the Vps17p PX domain is seen in many PX domains, no basic residues are found around the canonical phosphatidylinositol phosphate (PtdIns-P) binding site, suggesting an inability to bind PtdIns-P molecules.

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Organizational Affiliation: 

Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.75 kDa 
• Atom Count: 2,241 
• Modelled Residue Count: 248 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 17	A, B	139	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: VPS17, PEP21, YOR132W, O3314, YOR3314W
UniProt
Find proteins for P32913 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32913  Go to UniProtKB:  P32913

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.28	α = 90
b = 100.28	β = 90
c = 100.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-18 
Deposition Author(s): Maita, N., Kohda, D., Obita, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	16370050

Revision History  

• Version 1.0: 2022-05-18
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description