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- PDB-4m8z: Crystal Structure of SFH3, a phosphatidylinositol transfer protei... -

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Basic information

Entry
Database: PDB / ID: 4m8z
TitleCrystal Structure of SFH3, a phosphatidylinositol transfer protein that integrates phosphoinositide signaling with lipid droplet metabolism
ComponentsPhosphatidylinositol transfer protein PDR16
KeywordsSIGNALING PROTEIN / Lipid droplets / Phosphoinositides / meiosis / CRAL TRIO / SEC14 / phospholipid signaling
Function / homology
Function and homology information


negative regulation of sexual sporulation resulting in formation of a cellular spore / phosphatidylinositol transporter complex / phosphatidylinositol transfer activity / nucleus-vacuole junction / sterol binding / sterol biosynthetic process / phospholipid biosynthetic process / phospholipid transport / lipid droplet / cell periphery ...negative regulation of sexual sporulation resulting in formation of a cellular spore / phosphatidylinositol transporter complex / phosphatidylinositol transfer activity / nucleus-vacuole junction / sterol binding / sterol biosynthetic process / phospholipid biosynthetic process / phospholipid transport / lipid droplet / cell periphery / response to xenobiotic stimulus / endoplasmic reticulum membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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) ...: / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol transfer protein PDR16
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.928 Å
AuthorsOrtlund, E.O. / Pathak, M.C.
CitationJournal: Mol Biol Cell / Year: 2014
Title: A phosphatidylinositol transfer protein integrates phosphoinositide signaling with lipid droplet metabolism to regulate a developmental program of nutrient stress-induced membrane biogenesis.
Authors: Ren, J. / Pei-Chen Lin, C. / Pathak, M.C. / Temple, B.R. / Nile, A.H. / Mousley, C.J. / Duncan, M.C. / Eckert, D.M. / Leiker, T.J. / Ivanova, P.T. / Myers, D.S. / Murphy, R.C. / Brown, H.A. ...Authors: Ren, J. / Pei-Chen Lin, C. / Pathak, M.C. / Temple, B.R. / Nile, A.H. / Mousley, C.J. / Duncan, M.C. / Eckert, D.M. / Leiker, T.J. / Ivanova, P.T. / Myers, D.S. / Murphy, R.C. / Brown, H.A. / Verdaasdonk, J. / Bloom, K.S. / Ortlund, E.A. / Neiman, A.M. / Bankaitis, V.A.
History
DepositionAug 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol transfer protein PDR16
B: Phosphatidylinositol transfer protein PDR16


Theoretical massNumber of molelcules
Total (without water)82,0272
Polymers82,0272
Non-polymers00
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-24 kcal/mol
Surface area30850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.521, 114.716, 144.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 17 - 344 / Label seq-ID: 17 - 344

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Phosphatidylinositol transfer protein PDR16 / PITP / Pleiotropic drug resistance protein 16 / SEC14 homolog 3


Mass: 41013.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Gene: N1158, NP_014168.1. NM_001183069.1, PDR16, SFH3, YNL231C
Plasmid: pGEM_SFH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P53860
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: The reservoir solution consisted of 15 - 30% PEG 4000, 5% glycerol, 100 mM ammonium sulfate, 100 mM ammonium acetate pH 5.6. Thin plate-like crystals were harvested 3 - 4 days after mixing 2 ...Details: The reservoir solution consisted of 15 - 30% PEG 4000, 5% glycerol, 100 mM ammonium sulfate, 100 mM ammonium acetate pH 5.6. Thin plate-like crystals were harvested 3 - 4 days after mixing 2 ul protein solution (5 mg/ml) with 2 ul reservoir solution., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9782 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.93→89.89 Å / Num. all: 66699 / Num. obs: 66699 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.93-250.283199.9
2-2.085.10.2191100
2.08-2.175.10.1621100
2.17-2.295.10.1361100
2.29-2.435.10.1071100
2.43-2.625.10.0891100
2.62-2.885.10.0751100
2.88-3.35.10.0591100
3.3-4.1550.055199.6
4.15-304.90.048199.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1423refinement
SCALEPACKdata scaling
REFMAC5.8.0045refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
SGXPROphasing
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.928→28.427 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.21 / σ(F): 43.72 / Phase error: 29.47 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2507 3788 3 %
Rwork0.2177 --
obs0.2187 126276 99.13 %
all-66699 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.838 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0 Å2
2--0.39 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.928→28.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5271 0 0 495 5766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095447
X-RAY DIFFRACTIONf_angle_d1.1347375
X-RAY DIFFRACTIONf_dihedral_angle_d13.3482079
X-RAY DIFFRACTIONf_chiral_restr0.09799
X-RAY DIFFRACTIONf_plane_restr0.005941
Refine LS restraints NCS

Ens-ID: 1 / Number: 20681 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9279-1.95230.2651310.25624253X-RAY DIFFRACTION93
1.9523-1.9780.33081400.25994557X-RAY DIFFRACTION100
1.978-2.0050.29651470.25494584X-RAY DIFFRACTION100
2.005-2.03370.34631340.25194532X-RAY DIFFRACTION100
2.0337-2.0640.28071440.24474558X-RAY DIFFRACTION100
2.064-2.09630.28411460.22414592X-RAY DIFFRACTION99
2.0963-2.13060.2461450.22754516X-RAY DIFFRACTION100
2.1306-2.16740.2651430.21874594X-RAY DIFFRACTION100
2.1674-2.20680.27561370.21374589X-RAY DIFFRACTION100
2.2068-2.24920.26681390.21864478X-RAY DIFFRACTION99
2.2492-2.29510.24691420.21624623X-RAY DIFFRACTION99
2.2951-2.3450.24251410.21614479X-RAY DIFFRACTION100
2.345-2.39950.25621430.21344611X-RAY DIFFRACTION100
2.3995-2.45940.18371400.2074502X-RAY DIFFRACTION100
2.4594-2.52590.23551460.21314597X-RAY DIFFRACTION99
2.5259-2.60020.29021370.22484536X-RAY DIFFRACTION99
2.6002-2.68410.24881460.23444543X-RAY DIFFRACTION99
2.6841-2.77990.27741420.22554570X-RAY DIFFRACTION99
2.7799-2.89110.31281390.22914544X-RAY DIFFRACTION100
2.8911-3.02250.27361390.22494564X-RAY DIFFRACTION100
3.0225-3.18170.25921400.21954550X-RAY DIFFRACTION99
3.1817-3.38070.27281350.21874553X-RAY DIFFRACTION99
3.3807-3.64130.21951400.20214488X-RAY DIFFRACTION99
3.6413-4.00680.23421350.19954513X-RAY DIFFRACTION98
4.0068-4.58450.21641390.19394509X-RAY DIFFRACTION99
4.5845-5.76810.17611440.20434576X-RAY DIFFRACTION99
5.7681-28.43010.26191340.21884477X-RAY DIFFRACTION98

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