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- PDB-3vxw: Crystal structure of Saccharomyces cerevisiae Atg8 complexed with... -

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Basic information

Entry
Database: PDB / ID: 3vxw
TitleCrystal structure of Saccharomyces cerevisiae Atg8 complexed with Atg32 AIM
Components
  • Autophagy-related protein 8
  • Peptide from Autophagy-related protein 32
KeywordsPROTEIN TRANSPORT / ubiquitin fold / mitophagy
Function / homology
Function and homology information


mitochondria-nucleus signaling pathway / Cvt vesicle membrane / TBC/RABGAPs / Receptor Mediated Mitophagy / regulation of membrane invagination / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy ...mitochondria-nucleus signaling pathway / Cvt vesicle membrane / TBC/RABGAPs / Receptor Mediated Mitophagy / regulation of membrane invagination / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / cellular response to nitrogen starvation / phosphatidylethanolamine binding / protein-containing complex localization / fungal-type vacuole membrane / phagophore assembly site / reticulophagy / vacuolar membrane / autophagosome membrane / autophagosome assembly / autophagosome / regulation of macroautophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / mitochondrial membrane / macroautophagy / protein tag activity / autophagy / protein transport / mitochondrial outer membrane / membrane fusion / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 8 / Autophagy-related protein 32
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNoda, N.N. / Inagaki, F.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Autophagy-related protein 32 acts as autophagic degron and directly initiates mitophagy
Authors: Kondo-Okamoto, N. / Noda, N.N. / Suzuki, S.W. / Nakatogawa, H. / Takahashi, I. / Matsunami, M. / Hashimoto, A. / Inagaki, F. / Ohsumi, Y. / Okamoto, K.
History
DepositionSep 21, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autophagy-related protein 8
B: Peptide from Autophagy-related protein 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6824
Polymers14,4902
Non-polymers1922
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-36 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.836, 104.836, 104.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Autophagy-related protein 8 / Autophagy-related ubiquitin-like modifier ATG8 / Cytoplasm to vacuole targeting protein 5


Mass: 13757.894 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: APG8, ATG8, AUT7, CVT5, YBL0732, YBL078C / Plasmid: pHT1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P38182
#2: Protein/peptide Peptide from Autophagy-related protein 32 / / Extracellular mutant protein 37


Mass: 731.796 Da / Num. of mol.: 1 / Fragment: Atg8-family interacting motif / Source method: obtained synthetically
Details: This sequence corresponds to residues 86-90 of Saccharomyces cerevisiae Atg32
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40458
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 2.4M ammnonium sulfate, 0.1M sodium sulfate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 3969 / Num. obs: 3969 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rsym value: 0.069 / Net I/σ(I): 16.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.4 % / Num. unique all: 384 / Rsym value: 0.38 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZPN

2zpn


Resolution: 3→42.8 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 132387.04 / 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
Rfree0.272 394 10.1 %RANDOM
Rwork0.223 ---
all0.228 3969 --
obs0.223 3917 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.4316 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 64.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms911 0 10 5 926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 66 10.7 %
Rwork0.325 548 -
obs-614 95.8 %
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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