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- PDB-7zga: Structure of yeast Sec14p with ergoline -

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Basic information

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


negative regulation of phosphatidylcholine biosynthetic process / negative regulation of phosphatidylglycerol biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / ascospore formation / Golgi to vacuole transport / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / phospholipid transport ...negative regulation of phosphatidylcholine biosynthetic process / negative regulation of phosphatidylglycerol biosynthetic process / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / Golgi vesicle budding / ascospore formation / Golgi to vacuole transport / phosphatidylinositol metabolic process / Golgi to plasma membrane protein transport / phospholipid transport / Golgi membrane / Golgi apparatus / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Chem-IUF / SEC14 cytosolic factor
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 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

Downloads & links

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Assembly

Deposited unit
A: SEC14 cytosolic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5242
Polymers34,0181
Non-polymers5071
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14960 Å2
Unit cell
Length a, b, c (Å)87.498, 87.498, 110.068
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: 34017.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: SEC14, PIT1, YMR079W, YM9582.04 / Production host: Escherichia coli (E. coli) / References: UniProt: P24280
#2: Chemical ChemComp-IUF / ~{O}9-methyl ~{O}4-[2,2,2-tris(chloranyl)ethyl] (5~{a}~{S},6~{a}~{S},9~{R},10~{a}~{S})-7-methyl-3-nitro-5,5~{a},6,6~{a},8,9,10,10~{a}-octahydroindolo[4,3-fg]quinoline-4,9-dicarboxylate


Mass: 506.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22Cl3N3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
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: 2.3→44.529 Å / Num. obs: 41643 / % possible obs: 99.6 % / Redundancy: 4.5 % / Rrim(I) all: 0.094 / Net I/σ(I): 13.02
Reflection shellResolution: 2.3→6.83 Å / Num. unique obs: 41643 / Rrim(I) all: 0.094

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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: 2.302→44.529 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 2007 9.1 %
Rwork0.1883 --
obs0.1919 22066 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.302→44.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 32 77 2506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072422
X-RAY DIFFRACTIONf_angle_d1.0213297
X-RAY DIFFRACTIONf_dihedral_angle_d13.6651450
X-RAY DIFFRACTIONf_chiral_restr0.055350
X-RAY DIFFRACTIONf_plane_restr0.006432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.302-2.35910.32581360.26871354X-RAY DIFFRACTION97
2.3591-2.42290.25071440.24111421X-RAY DIFFRACTION100
2.4229-2.49410.29811410.22121431X-RAY DIFFRACTION100
2.4941-2.57460.2631430.22571409X-RAY DIFFRACTION100
2.5746-2.66660.25811410.20281397X-RAY DIFFRACTION100
2.6666-2.77340.24561370.2011413X-RAY DIFFRACTION100
2.7734-2.89960.27731430.20351437X-RAY DIFFRACTION100
2.8996-3.05240.25781430.19451432X-RAY DIFFRACTION100
3.0524-3.24360.27831440.20941432X-RAY DIFFRACTION100
3.2436-3.4940.23321410.19911429X-RAY DIFFRACTION100
3.494-3.84540.21491420.17641444X-RAY DIFFRACTION100
3.8454-4.40140.17211480.16151447X-RAY DIFFRACTION100
4.4014-5.54370.2241470.16291466X-RAY DIFFRACTION100
5.5437-44.5290.2091570.1881547X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.8216 Å / Origin y: 101.2479 Å / Origin z: 1.2943 Å
111213212223313233
T0.2993 Å2-0.0348 Å2-0.0046 Å2-0.3253 Å2-0.0185 Å2--0.2962 Å2
L0.7564 °20.2716 °2-0.5256 °2-1.6321 °2-0.4659 °2--0.7604 °2
S-0.0358 Å °0.0148 Å °-0.0279 Å °0.1324 Å °0.0458 Å °-0.0597 Å °-0.008 Å °-0.0135 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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