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- PDB-4tu3: Crystal structure of yeast Sac1/Vps74 complex -

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Basic information

Entry
Database: PDB / ID: 4tu3
TitleCrystal structure of yeast Sac1/Vps74 complex
Components
  • Phosphoinositide phosphatase SAC1
  • Vacuolar protein sorting-associated protein 74
KeywordsHYDROLASE/PROTEIN TRANSPORT / Protein Complex / Phosphoric Monoester Hydrolases / Phosphatidylinositol Phosphates / Golgi Apparatus / HYDROLASE-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


phosphatidylinositol-3-phosphatase / Synthesis of PIPs at the ER membrane / phosphatidylinositol-4-phosphate phosphatase activity / regulation of phosphatidylinositol dephosphorylation / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / host cell viral assembly compartment / phosphatidylinositol-3-phosphate phosphatase activity / Golgi vesicle budding / Synthesis of PIPs at the Golgi membrane / protein O-linked mannosylation ...phosphatidylinositol-3-phosphatase / Synthesis of PIPs at the ER membrane / phosphatidylinositol-4-phosphate phosphatase activity / regulation of phosphatidylinositol dephosphorylation / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / host cell viral assembly compartment / phosphatidylinositol-3-phosphate phosphatase activity / Golgi vesicle budding / Synthesis of PIPs at the Golgi membrane / protein O-linked mannosylation / serine palmitoyltransferase complex / intracellular sphingolipid homeostasis / Golgi cisterna / protein retention in Golgi apparatus / autophagosome-lysosome fusion / cortical endoplasmic reticulum / phosphatidylinositol dephosphorylation / Golgi to plasma membrane protein transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / protein N-linked glycosylation / phosphatidylinositol-4-phosphate binding / Golgi cisterna membrane / Golgi medial cisterna / Golgi organization / endoplasmic reticulum unfolded protein response / trans-Golgi network / mitochondrial outer membrane / Golgi membrane / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / Golgi apparatus / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
yeast vps74-n-term truncation variant fold / yeast vps74-n-term truncation variant domain like / Golgi phosphoprotein 3-like / Golgi phosphoprotein 3-like domain superfamily / Golgi phosphoprotein 3 (GPP34) / SAC domain / SacI homology domain / Sac phosphatase domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol-3-phosphatase SAC1 / Vacuolar protein sorting-associated protein 74
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.187 Å
AuthorsCai, Y. / Horenkamp, F.A. / Reinisch, K.R.
CitationJournal: J.Cell Biol. / Year: 2014
Title: Sac1-Vps74 structure reveals a mechanism to terminate phosphoinositide signaling in the Golgi apparatus.
Authors: Cai, Y. / Deng, Y. / Horenkamp, F. / Reinisch, K.M. / Burd, C.G.
History
DepositionJun 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Phosphoinositide phosphatase SAC1
A: Vacuolar protein sorting-associated protein 74


Theoretical massNumber of molelcules
Total (without water)110,5492
Polymers110,5492
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.338, 159.338, 143.389
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Phosphoinositide phosphatase SAC1 / Recessive suppressor of secretory defect


Mass: 71214.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SAC1, RSD1, YKL212W / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: P32368, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Protein Vacuolar protein sorting-associated protein 74


Mass: 39334.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VPS74, YDR372C, D9481.15 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q06385

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200mM HEPES at pH 7.0, 35% (v/v) MPD, 0.3M NDSB-195

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.187→29.542 Å / Num. obs: 22586 / % possible obs: 100 % / Redundancy: 9.8 % / Net I/σ(I): 18.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZIH, 3LWT

2zih

3lwt


Resolution: 3.187→29.542 Å / Cross valid method: NONE / σ(F): 2.01 / Phase error: 41.04 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2549 2003 8.87 %
Rwork0.226 --
obs0.2289 22586 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.187→29.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5191 0 0 0 5191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025285
X-RAY DIFFRACTIONf_angle_d0.4537174
X-RAY DIFFRACTIONf_dihedral_angle_d9.7471893
X-RAY DIFFRACTIONf_chiral_restr0.031832
X-RAY DIFFRACTIONf_plane_restr0.001923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1884-3.2680.37551390.37211433X-RAY DIFFRACTION88
3.268-3.35620.35511450.36471479X-RAY DIFFRACTION91
3.3562-3.45490.3411450.36161502X-RAY DIFFRACTION91
3.4549-3.56620.39231410.3441451X-RAY DIFFRACTION91
3.5662-3.69340.30251460.3231479X-RAY DIFFRACTION91
3.6934-3.84090.33661410.31531451X-RAY DIFFRACTION91
3.8409-4.01530.32851460.29721492X-RAY DIFFRACTION91
4.0153-4.22640.29061400.28381436X-RAY DIFFRACTION91
4.2264-4.49030.2841460.2551499X-RAY DIFFRACTION91
4.4903-4.83550.23031420.22211462X-RAY DIFFRACTION91
4.8355-5.31940.26311430.22561475X-RAY DIFFRACTION91
5.3194-6.0830.26481440.22681486X-RAY DIFFRACTION91
6.083-7.64050.23181420.20221454X-RAY DIFFRACTION91
7.6405-28.96090.17411430.12811475X-RAY DIFFRACTION91

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