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- PDB-3vp7: Crystal structure of the beta-alpha repeated, autophagy-specific ... -

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Basic information

Entry
Database: PDB / ID: 3vp7
TitleCrystal structure of the beta-alpha repeated, autophagy-specific (BARA) domain of Vps30/Atg6
ComponentsVacuolar protein sorting-associated protein 30
KeywordsPROTEIN TRANSPORT / targeting / PI3-kinase complex I / pre-autophagosomal structure
Function / homology
Function and homology information


vacuole-isolation membrane contact site / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / pexophagy / phagophore assembly site membrane / protein targeting to vacuole / late endosome to vacuole transport / piecemeal microautophagy of the nucleus ...vacuole-isolation membrane contact site / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / pexophagy / phagophore assembly site membrane / protein targeting to vacuole / late endosome to vacuole transport / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / phosphatidylinositol biosynthetic process / fungal-type vacuole membrane / retrograde transport, endosome to Golgi / phagophore assembly site / phosphatidylinositol phosphate biosynthetic process / autophagosome assembly / macroautophagy / autophagy / protein transport / endosome membrane / Golgi membrane / cytoplasm / cytosol
Similarity search - Function
Autophagy protein 6/Beclin 1 / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Actin-binding Protein, T-fimbrin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 30
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsNoda, N.N. / Kobayashi, T. / Adachi, W. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of the novel C-terminal domain of vacuolar protein sorting 30/autophagy-related protein 6 and its specific role in autophagy.
Authors: Noda, N.N. / Kobayashi, T. / Adachi, W. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F.
History
DepositionFeb 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 30


Theoretical massNumber of molelcules
Total (without water)24,6811
Polymers24,6811
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Vacuolar protein sorting-associated protein 30

A: Vacuolar protein sorting-associated protein 30


Theoretical massNumber of molelcules
Total (without water)49,3622
Polymers49,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1800 Å2
ΔGint-18 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.959, 59.959, 113.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-626-

HOH

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Components

#1: Protein Vacuolar protein sorting-associated protein 30 / Autophagy-related protein 6


Mass: 24681.158 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP RESIDUES 320-539
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VPS30, APG6, ATG6, VPT30, YPL120W, LPH7 / Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02948
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.5M sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.967 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.3→34.02 Å / Num. all: 9850 / Num. obs: 9844 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.325 / Num. unique all: 946 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→34 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 111100.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.243 987 10.4 %RANDOM
Rwork0.209 ---
all0.212 9787 --
obs0.209 9484 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5917 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1--3.36 Å20 Å20 Å2
2---3.36 Å20 Å2
3---6.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 0 42 1353
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 172 11.7 %
Rwork0.233 1303 -
obs-1475 93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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