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- PDB-7zgd: Structure of yeast Sec14p with NPPM244 -

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Basic information

Entry
Database: PDB / ID: 7zgd
TitleStructure of yeast Sec14p with NPPM244
ComponentsSEC14 cytosolic factor
KeywordsLIPID BINDING PROTEIN / Sec14p / NPPM244
Function / homology
Function and homology information


negative regulation of phosphatidylglycerol biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / Golgi to vacuole transport / ascospore formation / post-Golgi vesicle-mediated transport / phosphatidylinositol metabolic process / phospholipid transport ...negative regulation of phosphatidylglycerol biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / Golgi to vacuole transport / ascospore formation / post-Golgi vesicle-mediated transport / phosphatidylinositol metabolic process / phospholipid transport / Golgi to plasma membrane protein transport / Golgi membrane / Golgi apparatus / cytoplasm / cytosol
Similarity search - Function
: / N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. ...: / N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-IUC / SEC14 cytosolic factor
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsHong, Z. / Johnen, P. / Schaaf, G. / Bono, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Mechanisms by which small molecules of diverse chemotypes arrest Sec14 lipid transfer activity.
Authors: Chen, X.R. / Poudel, L. / Hong, Z. / Johnen, P. / Katti, S. / Tripathi, A. / Nile, A.H. / Green, S.M. / Khan, D. / Schaaf, G. / Bono, F. / Bankaitis, V.A. / Igumenova, T.I.
History
DepositionApr 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SEC14 cytosolic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4562
Polymers36,0481
Non-polymers4081
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.728, 86.728, 109.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein SEC14 cytosolic factor / Phosphatidylinositol/phosphatidylcholine transfer protein / PI/PC TP


Mass: 36047.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SEC14, PIT1, YMR079W, YM9582.04 / Production host: Escherichia coli (E. coli) / References: UniProt: P24280
#2: Chemical ChemComp-IUC / (4-bromanyl-3-nitro-phenyl)-[4-(2-fluorophenyl)piperazin-1-yl]methanone


Mass: 408.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15BrFN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 294 K / Method: evaporation
Details: 129,5 mM sodium acetate, 64,8 mM TRIS, 4,6 % (w/v) PEG 4000, and 11.9 % (v/v) glycerol adjusted to pH 7.0

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Data collection

DiffractionMean temperature: 124 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→44.272 Å / Num. obs: 55450 / % possible obs: 100 % / Redundancy: 10.4 % / Rrim(I) all: 0.109 / Net I/σ(I): 14.52
Reflection shellResolution: 2.08→6.19 Å / Num. unique obs: 55450 / Rrim(I) all: 0.104

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1aua

1aua


Resolution: 2.08→44.272 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 2773 5 %
Rwork0.1976 --
obs0.1992 55416 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→44.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 25 23 2441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082489
X-RAY DIFFRACTIONf_angle_d0.8953366
X-RAY DIFFRACTIONf_dihedral_angle_d14.6751503
X-RAY DIFFRACTIONf_chiral_restr0.055345
X-RAY DIFFRACTIONf_plane_restr0.006441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.11580.31471410.29592677X-RAY DIFFRACTION100
2.1158-2.15430.30171390.28282579X-RAY DIFFRACTION100
2.1543-2.19570.33131380.27032616X-RAY DIFFRACTION100
2.1957-2.24050.28041370.2592658X-RAY DIFFRACTION100
2.2405-2.28920.26511380.2452654X-RAY DIFFRACTION100
2.2892-2.34250.28671360.24712618X-RAY DIFFRACTION100
2.3425-2.40110.27041350.23542644X-RAY DIFFRACTION100
2.4011-2.4660.27591400.23222616X-RAY DIFFRACTION100
2.466-2.53850.28941390.23672658X-RAY DIFFRACTION100
2.5385-2.62050.29971370.21652621X-RAY DIFFRACTION100
2.6205-2.71410.2141370.20982616X-RAY DIFFRACTION100
2.7141-2.82280.29731390.22012625X-RAY DIFFRACTION100
2.8228-2.95120.25431400.22562633X-RAY DIFFRACTION100
2.9512-3.10680.2571410.23252655X-RAY DIFFRACTION100
3.1068-3.30130.28531370.23032605X-RAY DIFFRACTION100
3.3013-3.55610.2481360.20172622X-RAY DIFFRACTION100
3.5561-3.91380.23471460.1822649X-RAY DIFFRACTION100
3.9138-4.47970.18961390.16252613X-RAY DIFFRACTION100
4.4797-5.64210.17551400.15922629X-RAY DIFFRACTION100
5.6421-44.270.18171380.16642655X-RAY DIFFRACTION100

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