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- PDB-7zg9: Structure of yeast Sec14p with himbacine -

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Basic information

Entry
Database: PDB / ID: 7zg9
TitleStructure of yeast Sec14p with himbacine
ComponentsSEC14 cytosolic factor
KeywordsLIPID BINDING PROTEIN / Sec14p / himbacine
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
Himbacine / SEC14 cytosolic factor
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.764 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
B: SEC14 cytosolic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6164
Polymers67,9252
Non-polymers6912
Water3,981221
1
A: SEC14 cytosolic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3082
Polymers33,9631
Non-polymers3461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SEC14 cytosolic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3082
Polymers33,9631
Non-polymers3461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.593, 86.593, 148.746
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: 33962.512 Da / Num. of mol.: 2
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-KO0 / Himbacine / (3S,3aR,4S,4R,8aR,9aS)-4-[(E)-2-[(2R,6S)-1,6-dimethylpiperidin-2-yl]ethenyl]-3-methyl-3a,4,4a,5,6,7,8,8a,9,9a-decahydro-3H-benzo[f][2]benzofuran-1-one


Mass: 345.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H35NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
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, pH 7.0

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Data collection

DiffractionMean temperature: 238 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: 1.76→43.297 Å / Num. obs: 122833 / % possible obs: 100 % / Redundancy: 10.1 % / Rrim(I) all: 0.072 / Net I/σ(I): 19.16
Reflection shellResolution: 1.76→5.26 Å / Num. unique obs: 122833 / Rrim(I) all: 0.072

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1aua

1aua


Resolution: 1.764→43.297 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 6109 4.98 %
Rwork0.1949 --
obs0.1963 122777 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.764→43.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 50 221 5046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124954
X-RAY DIFFRACTIONf_angle_d1.0886703
X-RAY DIFFRACTIONf_dihedral_angle_d19.5781864
X-RAY DIFFRACTIONf_chiral_restr0.154708
X-RAY DIFFRACTIONf_plane_restr0.008864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7641-1.78420.35632020.3273787X-RAY DIFFRACTION99
1.7842-1.80520.33312060.2963981X-RAY DIFFRACTION100
1.8052-1.82720.3132030.28333833X-RAY DIFFRACTION100
1.8272-1.85030.28442040.2683946X-RAY DIFFRACTION100
1.8503-1.87470.3072030.2693821X-RAY DIFFRACTION100
1.8747-1.90030.26722090.25813924X-RAY DIFFRACTION100
1.9003-1.92750.29782000.26133870X-RAY DIFFRACTION100
1.9275-1.95630.26931970.24763879X-RAY DIFFRACTION100
1.9563-1.98680.26072040.23643881X-RAY DIFFRACTION100
1.9868-2.01940.26652070.22363923X-RAY DIFFRACTION100
2.0194-2.05420.2682080.22533923X-RAY DIFFRACTION100
2.0542-2.09160.21671980.21243836X-RAY DIFFRACTION100
2.0916-2.13180.21392060.20693904X-RAY DIFFRACTION100
2.1318-2.17530.23012040.20243916X-RAY DIFFRACTION100
2.1753-2.22260.2412050.213900X-RAY DIFFRACTION100
2.2226-2.27430.25282040.21653874X-RAY DIFFRACTION100
2.2743-2.33120.24732010.19793893X-RAY DIFFRACTION100
2.3312-2.39420.25222040.21523880X-RAY DIFFRACTION100
2.3942-2.46470.22682030.20163908X-RAY DIFFRACTION100
2.4647-2.54420.26792040.20673902X-RAY DIFFRACTION100
2.5442-2.63510.24712070.20433847X-RAY DIFFRACTION100
2.6351-2.74060.24151980.19823903X-RAY DIFFRACTION100
2.7406-2.86530.22962050.20393909X-RAY DIFFRACTION100
2.8653-3.01630.22772040.19683863X-RAY DIFFRACTION100
3.0163-3.20530.26582050.19573911X-RAY DIFFRACTION100
3.2053-3.45270.17792000.17793903X-RAY DIFFRACTION100
3.4527-3.79990.19072030.17793852X-RAY DIFFRACTION100
3.7999-4.34930.19652030.16353919X-RAY DIFFRACTION100
4.3493-5.4780.2042060.16533878X-RAY DIFFRACTION100
5.478-43.2970.18222060.18223902X-RAY DIFFRACTION100

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