9EFP | pdb_00009efp

Crystal Structure of Saccharomyces cerevisiae Sec14p in complex with phosphatidylcholine

PDB DOI: https://doi.org/10.2210/pdb9EFP/pdb

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

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: 1.83 Å
R-Value Free:
0.208 (Depositor), 0.201 (DCC)
R-Value Work:
0.172 (Depositor), 0.175 (DCC)
R-Value Observed:
0.186 (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 Sec14p in complex with phosphatidylcholine

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: 72.12 kDa
Atom Count: 5,126
Modeled Residue Count: 579
Deposited Residue Count: 608
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SEC14 cytosolic factor	A, B	304	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SEC14, PIT1, YMR079W, YM9582.04
UniProt
Find proteins for P24280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P24280 Go to UniProtKB: P24280
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24280
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV (Subject of Investigation/LOI) Query on POV Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	G [auth B], H [auth B], I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.208 (Depositor), 0.201 (DCC)
R-Value Work: 0.172 (Depositor), 0.175 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.4	α = 90
b = 74.4	β = 90
c = 195.86	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
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