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- PDB-3gre: Crystal structure of Saccharomyces cerevisiae Vps15 WD repeat domain -

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Basic information

Entry
Database: PDB / ID: 3gre
TitleCrystal structure of Saccharomyces cerevisiae Vps15 WD repeat domain
ComponentsSerine/threonine-protein kinase VPS15
KeywordsSIGNALING PROTEIN / PROTEIN BINDING / seven-bladed propeller / WD repeat / scaffold protein / ATP-binding / Endosome / Golgi apparatus / Kinase / Lipoprotein / Membrane / Myristate / Nucleotide-binding / Phosphoprotein / Protein transport / Serine/threonine-protein kinase / Transferase / Transport
Function / homology
Function and homology information


Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / RHO GTPases Activate NADPH Oxidases / nucleus-vacuole junction / vacuole-isolation membrane contact site / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / vacuole inheritance / cellular response to potassium ion starvation ...Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / RHO GTPases Activate NADPH Oxidases / nucleus-vacuole junction / vacuole-isolation membrane contact site / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / vacuole inheritance / cellular response to potassium ion starvation / Macroautophagy / protein retention in Golgi apparatus / phagophore assembly site membrane / protein targeting to vacuole / late endosome to vacuole transport / pexophagy / fungal-type vacuole membrane / phosphatidylinositol phosphate biosynthetic process / ubiquitin binding / positive regulation of transcription elongation by RNA polymerase II / macroautophagy / autophagy / late endosome / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / endosome membrane / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding
Similarity search - Function
Vps8 beta-propeller / Serine/threonine-protein kinase Vps15-like / : / VPS15-like, helical domain / HEAT repeat profile. / HEAT, type 2 / Armadillo-like helical / Armadillo-type fold / Trp-Asp (WD) repeats profile. / WD40 repeats ...Vps8 beta-propeller / Serine/threonine-protein kinase Vps15-like / : / VPS15-like, helical domain / HEAT repeat profile. / HEAT, type 2 / Armadillo-like helical / Armadillo-type fold / Trp-Asp (WD) repeats profile. / WD40 repeats / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40 repeat / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase VPS15
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsVanhooke, J.L. / Sondek, J. / Betts, L.
CitationJournal: Biochemistry / Year: 2009
Title: Structure and function of Vps15 in the endosomal G protein signaling pathway.
Authors: Heenan, E.J. / Vanhooke, J.L. / Temple, B.R. / Betts, L. / Sondek, J.E. / Dohlman, H.G.
History
DepositionMar 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase VPS15


Theoretical massNumber of molelcules
Total (without water)48,9511
Polymers48,9511
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.493, 85.493, 132.821
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Serine/threonine-protein kinase VPS15 / Vacuolar protein sorting-associated protein 15 / Golgi-retention defective mutant protein 8


Mass: 48950.805 Da / Num. of mol.: 1 / Fragment: WD repeat domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: BY4741 / Gene: GRD8, VAC4, VPL19, VPS15, YBR0825, YBR097W / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P22219, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 291 K / Method: macroseeding into microbatch / pH: 6.5
Details: 0.7 M ammonium malonate, 0.05 M sodium acetate, 2% 2-propanol, pH 6.5, macroseeding into microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2007
RadiationMonochromator: Double crystal monochromator, Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 21.5 % / Av σ(I) over netI: 36 / Number: 637020 / Rmerge(I) obs: 0.097 / Χ2: 1.03 / D res high: 2.2 Å / D res low: 30 Å / Num. obs: 29652 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.963099.810.0771.98218.6
4.735.9610010.0771.62720.3
4.144.7310010.0761.46420.6
3.764.1410010.0851.55920.8
3.493.7610010.091.55920.9
3.293.4910010.091.35921.4
3.123.2910010.0931.21921.8
2.993.1210010.1021.10121.8
2.872.9910010.1111.02721.9
2.772.8710010.1170.90522
2.682.7710010.1270.87622
2.612.6810010.1380.79422
2.542.6110010.150.74722
2.482.5410010.1610.71222
2.422.4810010.1770.66822.1
2.372.4210010.1870.65821.9
2.322.3710010.1970.63122
2.282.3210010.2060.63622.1
2.242.2810010.2230.65421.9
2.22.2410010.2490.6122
ReflectionResolution: 1.8→50 Å / Num. all: 50964 / Num. obs: 50964 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Rmerge(I) obs: 0.081 / Χ2: 1.059 / Net I/σ(I): 36.003
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3714 / Rsym value: 0.527 / Χ2: 0.457 / % possible all: 71.2

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 74.54 Å / FOM : 0.284 / FOM acentric: 0.323 / FOM centric: 0 / Reflection: 20297 / Reflection acentric: 17861 / Reflection centric: 2436
Phasing MAD setR cullis acentric: 1.97 / R cullis centric: 1 / Highest resolution: 2.5 Å / Lowest resolution: 74.54 Å / Loc acentric: 0.1 / Loc centric: 0 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 17861 / Reflection centric: 2436
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
16.2-74.541.450.10.14242
9.09-16.21.120.10.1266121
6.31-9.091.930.10.1693196
4.84-6.311.630.101311274
3.92-4.841.290.10.12133336
3.3-3.921.460.103166424
2.84-3.32.360.104412492
2.5-2.844.31005838551
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
16.2-74.540.0460.0910844242
9.09-16.20.2270.3290387266121
6.31-9.090.2630.3380889693196
4.84-6.310.3220.389015851311274
3.92-4.840.3090.357024692133336
3.3-3.920.3160.358035903166424
2.84-3.30.2980.331049044412492
2.5-2.840.2470.27063895838551
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 29627
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.9-10077.90.2502
6.98-8.9680.778517
6.02-6.9862.50.841541
5.38-6.0260.20.852603
4.9-5.3863.30.879680
4.53-4.962.80.885705
4.24-4.5365.60.89799
3.99-4.2464.50.875807
3.78-3.99620.875864
3.61-3.7864.90.881907
3.45-3.6163.80.867948
3.32-3.4563.90.879978
3.19-3.3265.90.8741028
3.09-3.1961.70.8861063
2.99-3.0963.60.8381082
2.9-2.9962.60.8391142
2.82-2.963.80.8471155
2.74-2.8265.10.8461191
2.67-2.7462.60.8371218
2.61-2.6765.50.831252
2.55-2.6164.40.8291287
2.49-2.55690.821299
2.44-2.49910.7981327
2.39-2.4491.40.791369
2.34-2.3991.40.81386
2.3-2.3488.30.8081401
2.26-2.390.30.7841436
2.2-2.2690.50.7192140

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.8→49.44 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.822 / SU B: 2.933 / SU ML: 0.09 / SU R Cruickshank DPI: 0.12 / SU Rfree: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.12 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2592 5.1 %RANDOM
Rwork0.209 ---
all0.211 50917 --
obs0.211 50917 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.08 Å2 / Biso mean: 35.727 Å2 / Biso min: 17.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20.86 Å20 Å2
2--1.72 Å20 Å2
3----2.58 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 0 200 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223231
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9574400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5625418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35424.776134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05115554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7751515
X-RAY DIFFRACTIONr_chiral_restr0.1160.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022391
X-RAY DIFFRACTIONr_nbd_refined0.2160.21349
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22261
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.216
X-RAY DIFFRACTIONr_mcbond_it0.9841.52105
X-RAY DIFFRACTIONr_mcangle_it1.71723348
X-RAY DIFFRACTIONr_scbond_it2.26331254
X-RAY DIFFRACTIONr_scangle_it3.5414.51045
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 132 -
Rwork0.287 2499 -
all-2631 -
obs-2499 68.23 %

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