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- PDB-2zpn: The crystal structure of Saccharomyces cerevisiae Atg8- Atg19(412... -

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Basic information

Entry
Database: PDB / ID: 2zpn
TitleThe crystal structure of Saccharomyces cerevisiae Atg8- Atg19(412-415) complex
Components
  • Autophagy-related protein 8
  • Saccharomyces cerevisiae Atg19(412-415)
KeywordsPROTEIN TRANSPORT / ubiquitin fold / Autophagy / Cytoplasmic vesicle / Lipoprotein / Membrane / Transport / Ubl conjugation pathway / Vacuole
Function / homology
Function and homology information


Cvt vesicle membrane / Cvt complex / TBC/RABGAPs / Receptor Mediated Mitophagy / regulation of membrane invagination / vacuole-isolation membrane contact site / lipid droplet formation / protein targeting to vacuole involved in autophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway ...Cvt vesicle membrane / Cvt complex / TBC/RABGAPs / Receptor Mediated Mitophagy / regulation of membrane invagination / vacuole-isolation membrane contact site / lipid droplet formation / protein targeting to vacuole involved in autophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / vesicle organization / protein localization to phagophore assembly site / phagophore assembly site membrane / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phosphatidylethanolamine binding / protein-containing complex localization / phagophore assembly site / fungal-type vacuole membrane / cellular response to nitrogen starvation / reticulophagy / autophagosome membrane / autophagosome assembly / autophagosome maturation / regulation of macroautophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / mitophagy / ERAD pathway / lipid droplet / autophagosome / mitochondrial membrane / autophagy / protein tag activity / protein transport / protein-macromolecule adaptor activity / membrane fusion / cytoplasm / cytosol
Similarity search - Function
Autophagy protein Atg19/Atg34, C-terminal / Autophagy protein Atg19, Atg8-binding / 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 19 / Autophagy-related protein 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNoda, N.N. / Inagaki, F.
CitationJournal: Genes Cells / Year: 2008
Title: Structural basis of target recognition by Atg8/LC3 during selective autophagy
Authors: Noda, N.N. / Kumeta, H. / Nakatogawa, H. / Satoo, K. / Adachi, W. / Ishii, J. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F.
History
DepositionJul 17, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Autophagy-related protein 8
B: Autophagy-related protein 8
C: Autophagy-related protein 8
D: Autophagy-related protein 8
E: Saccharomyces cerevisiae Atg19(412-415)
F: Saccharomyces cerevisiae Atg19(412-415)
G: Saccharomyces cerevisiae Atg19(412-415)
H: Saccharomyces cerevisiae Atg19(412-415)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,81413
Polymers57,3348
Non-polymers4805
Water39622
1
A: Autophagy-related protein 8
E: Saccharomyces cerevisiae Atg19(412-415)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5264
Polymers14,3342
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-19.1 kcal/mol
Surface area6930 Å2
MethodPISA
2
B: Autophagy-related protein 8
F: Saccharomyces cerevisiae Atg19(412-415)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4303
Polymers14,3342
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-29.3 kcal/mol
Surface area6520 Å2
MethodPISA
3
C: Autophagy-related protein 8
G: Saccharomyces cerevisiae Atg19(412-415)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4303
Polymers14,3342
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-19.4 kcal/mol
Surface area6600 Å2
MethodPISA
4
D: Autophagy-related protein 8
H: Saccharomyces cerevisiae Atg19(412-415)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4303
Polymers14,3342
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-21 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.150, 104.450, 113.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732 / Plasmid: pHT1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P38182
#2: Protein/peptide
Saccharomyces cerevisiae Atg19(412-415)


Mass: 575.610 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: This sequence corresponds to residues 412-415 of Saccharomyces cerevisiae Atg19.
References: UniProt: P35193*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 2.0M ammonium sulfate, 0.1M sodium citrate, pH4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→41.1 Å / Num. all: 14927 / Num. obs: 14927 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.12 / Num. unique all: 1494 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GNU

1gnu


Resolution: 2.7→41.1 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 84615.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1476 10.2 %RANDOM
Rwork0.242 ---
obs0.242 14505 96.8 %-
all-14505 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.0308 Å2 / ksol: 0.371913 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.9 Å20 Å20 Å2
2--0.15 Å20 Å2
3---5.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.7→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 25 22 3611
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 239 10.6 %
Rwork0.292 2007 -
obs-2246 92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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