9EFN | pdb_00009efn

Crystal structure of Saccharomyces cerevisiae cross-linked Sfh1 (K197C, F233C) mutant in complex with phosphatidylethanolamine

PDB DOI: https://doi.org/10.2210/pdb9EFN/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-11-20 Released: 2025-11-05
Deposition Author(s): Green, S.M., Laganowsky, A., Krieger, I., Singh, P.K., Sacchettini, J., Igumenova, T.I., Bankaitis, V.A.
Funding Organization(s): Welch Foundation, Robert A. Welch Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.279 (Depositor), 0.280 (DCC)
R-Value Work:
0.241 (Depositor), 0.242 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Saccharomyces cerevisiae cross-linked Sfh1 (K197C, F233C) mutant in complex with phosphatidylethanolamine

Green, S.M., Laganowsky, A., Krieger, I., Singh, P.K., Sacchettini, J., Igumenova, T.I., Bankaitis, V.A.

To be published.

Macromolecule Content

Total Structure Weight: 74.41 kDa
Atom Count: 5,817
Modeled Residue Count: 618
Deposited Residue Count: 620
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRAL-TRIO domain-containing protein YKL091C	A, B	310	Saccharomyces cerevisiae	Mutation(s): 3 Gene Names: YKL091C
UniProt
Find proteins for P33324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33324 Go to UniProtKB: P33324
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33324
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY (Subject of Investigation/LOI) Query on PTY Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] K [auth B] D [auth A], E [auth A], F [auth A], G [auth A], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.279 (Depositor), 0.280 (DCC)
R-Value Work: 0.241 (Depositor), 0.242 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.43	α = 90
b = 72.01	β = 93.95
c = 114.68	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Welch Foundation	United States	A-2194-20240404
Robert A. Welch Foundation	United States	BE-0017
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH R35 GM131804
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH RO1 GM108998