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- PDB-2dym: The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-4... -

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Basic information

Entry
Database: PDB / ID: 2dym
TitleThe crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex
Components
  • Autophagy protein 16
  • Autophagy protein 5
KeywordsPROTEIN TURNOVER/PROTEIN TURNOVER / ubiquitin-fold / herix-bundle / PROTEIN TURNOVER-PROTEIN TURNOVER COMPLEX
Function / homology
Function and homology information


Receptor Mediated Mitophagy / cargo receptor ligand activity / Atg12-Atg5-Atg16 complex / vacuole-isolation membrane contact site / phagophore / cellular response to potassium ion starvation / Macroautophagy / mitochondria-associated endoplasmic reticulum membrane contact site / transferase complex / cytoplasm to vacuole targeting by the Cvt pathway ...Receptor Mediated Mitophagy / cargo receptor ligand activity / Atg12-Atg5-Atg16 complex / vacuole-isolation membrane contact site / phagophore / cellular response to potassium ion starvation / Macroautophagy / mitochondria-associated endoplasmic reticulum membrane contact site / transferase complex / cytoplasm to vacuole targeting by the Cvt pathway / autophagosome organization / nucleophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / cellular response to nitrogen starvation / autophagy of mitochondrion / autophagosome assembly / mitophagy / enzyme activator activity / autophagosome / macroautophagy / autophagy / protein-macromolecule adaptor activity / hydrolase activity / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / : / : / : / Autophagy protein ATG5, UblB domain / Autophagy protein ATG5, alpha-helical bundle region ...Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / : / : / : / Autophagy protein ATG5, UblB domain / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Serum Albumin; Chain A, Domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Autophagy protein 16 / Autophagy protein 5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MAD / Resolution: 2.2 Å
AuthorsMatsushita, M. / Suzuki, N.N. / Inagaki, F.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Structure of Atg5.Atg16, a complex essential for autophagy
Authors: Matsushita, M. / Suzuki, N.N. / Obara, K. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Expression, purification and crystallization of the Atg5-Atg16 complex essential for autophagy
Authors: Matsushita, M. / Suzuki, N.N. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F.
History
DepositionSep 15, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: Autophagy protein 5
B: Autophagy protein 16
C: Autophagy protein 5
D: Autophagy protein 16
E: Autophagy protein 5
F: Autophagy protein 16
G: Autophagy protein 5
H: Autophagy protein 16


Theoretical massNumber of molelcules
Total (without water)157,4498
Polymers157,4498
Non-polymers00
Water5,783321
1
A: Autophagy protein 5
B: Autophagy protein 16


Theoretical massNumber of molelcules
Total (without water)39,3622
Polymers39,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-12 kcal/mol
Surface area13440 Å2
MethodPISA
2
C: Autophagy protein 5
D: Autophagy protein 16


Theoretical massNumber of molelcules
Total (without water)39,3622
Polymers39,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-14 kcal/mol
Surface area13680 Å2
MethodPISA
3
E: Autophagy protein 5
F: Autophagy protein 16


Theoretical massNumber of molelcules
Total (without water)39,3622
Polymers39,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-13 kcal/mol
Surface area13210 Å2
MethodPISA
4
G: Autophagy protein 5
H: Autophagy protein 16


Theoretical massNumber of molelcules
Total (without water)39,3622
Polymers39,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-11 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.347, 104.417, 112.153
Angle α, β, γ (deg.)90.00, 92.11, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a hetero-dimer consisting of chain A and B, C and D, E and F, or G and H.

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Components

#1: Protein
Autophagy protein 5


Mass: 33862.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATG5 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12380
#2: Protein/peptide
Autophagy protein 16 / Cytoplasm to vacuole targeting protein 11 / SAP18 homolog


Mass: 5500.188 Da / Num. of mol.: 4 / Fragment: residues 1-46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATG16 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03818
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 24% PEG 3350, 0.1M CAPS, pH 10, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 88015 / Num. obs: 88015 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.306 / % possible all: 95.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MIR, MAD / Resolution: 2.2→49.38 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 408111.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 7451 10 %RANDOM
Rwork0.219 ---
all0.222 74879 --
obs0.219 74879 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.4423 Å2 / ksol: 0.352691 e/Å3
Displacement parametersBiso mean: 44.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.84 Å20 Å2-7.08 Å2
2--2.23 Å20 Å2
3---6.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8875 0 0 321 9196
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.772
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.362.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 1153 9.9 %
Rwork0.261 10545 -
obs-11697 90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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