6SLD

Structure of the Phosphatidylcholine Binding Mutant of Yeast Sec14 Homolog Sfh1 (S175I,T177I) in Complex with Phosphatidylinositol

• PDB DOI: https://doi.org/10.2210/pdb6SLD/pdb

• Classification: LIPID TRANSPORT
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-08-19 Released: 2020-08-19 
• Deposition Author(s): Berger, J., Fitz, M., Johnen, P., Shanmugaratnam, S., Hocker, B., Stiel, A.C., Schaaf, G.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.164 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 

Literature

Structure of the Phosphatidylcholine Binding Mutant of Yeast Sec14 Homolog Sfh1 (S175I,T177I) in Complex with Phosphatidylinositol

Berger, J., Fitz, M., Johnen, P., Shanmugaratnam, S., Hocker, B., Stiel, A.C., Schaaf, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.69 kDa 
• Atom Count: 2,982 
• Modelled Residue Count: 307 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRAL-TRIO domain-containing protein YKL091C	A	307	Saccharomyces cerevisiae S288C	Mutation(s): 2  Gene Names: YKL091C
UniProt
Find proteins for P33324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33324  Go to UniProtKB:  P33324

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B7N (Subject of Investigation/LOI)	B [auth A]	(1R)-2-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C45 H85 O13 P YOBFISPJJWPPTK-BAAZTTAESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.164 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.22	α = 90
b = 70.81	β = 90
c = 90.19	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Berger, J., Fitz, M., Johnen, P., Shanmugaratnam, S., Hocker, B., Stiel, A.C., Schaaf, G.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	Emmy Noether grant 1274/2-1
German Research Foundation	Germany	SCHA 1274/5-1
German Research Foundation	Germany	GRK 2064
German Research Foundation	Germany	Germany's Excellence Strategy, EXC-2070_390732324_PhenoRob

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references