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- PDB-3w1s: Crystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugat... -

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Basic information

Entry
Database: PDB / ID: 3w1s
TitleCrystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugate bound to the N-terminal domain of Atg16
Components
  • Autophagy protein 16
  • Autophagy protein 5
  • Ubiquitin-like protein ATG12
KeywordsLIGASE / Ubiquitin fold / E3-like / Atg3 binding / Isopeptide bond between Atg12 Gly186 and Atg5 Lys149
Function / homology
Function and homology information


protein lipidation involved in autophagosome assembly / cargo receptor ligand activity / Receptor Mediated Mitophagy / Atg8-family ligase activity / phagophore / Atg12-Atg5-Atg16 complex / : / C-terminal protein lipidation / vacuole-isolation membrane contact site / : ...protein lipidation involved in autophagosome assembly / cargo receptor ligand activity / Receptor Mediated Mitophagy / Atg8-family ligase activity / phagophore / Atg12-Atg5-Atg16 complex / : / C-terminal protein lipidation / vacuole-isolation membrane contact site / : / Macroautophagy / transferase complex / cytoplasm to vacuole targeting by the Cvt pathway / autophagosome organization / nucleophagy / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / cellular response to nitrogen starvation / autophagy of mitochondrion / phagophore assembly site / autophagosome assembly / enzyme activator activity / autophagosome / macroautophagy / protein tag activity / autophagy / protein-macromolecule adaptor activity / protein transport / hydrolase activity / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / : / : / : / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Autophagy-related protein 5 ...Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / : / : / : / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / Autophagy protein ATG5, UblB 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) / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein ATG12 / Autophagy protein 16 / Autophagy protein 5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNoda, N.N. / Fujioka, Y. / Hanada, T. / Ohsumi, Y. / Inagaki, F.
CitationJournal: Embo Rep. / Year: 2013
Title: Structure of the Atg12-Atg5 conjugate reveals a platform for stimulating Atg8-PE conjugation
Authors: Noda, N.N. / Fujioka, Y. / Hanada, T. / Ohsumi, Y. / Inagaki, F.
History
DepositionNov 20, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / 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
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: Ubiquitin-like protein ATG12


Theoretical massNumber of molelcules
Total (without water)48,7543
Polymers48,7543
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Autophagy protein 5
B: Autophagy protein 16
C: Ubiquitin-like protein ATG12

A: Autophagy protein 5
B: Autophagy protein 16
C: Ubiquitin-like protein ATG12


Theoretical massNumber of molelcules
Total (without water)97,5096
Polymers97,5096
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9900 Å2
ΔGint-46 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.149, 106.084, 143.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Autophagy protein 5 /


Mass: 32620.820 Da / Num. of mol.: 1 / Fragment: UNP residues 1-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: APG5, ATG5, Atg5(amino acids 1-284), P2601, YPL149W / Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12380
#2: Protein/peptide Autophagy protein 16 / / Cytoplasm to vacuole targeting protein 11 / SAP18 homolog


Mass: 5792.501 Da / Num. of mol.: 1 / Fragment: UNP residues 1-46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Gene: APG15, APG16, ATG16, Atg16(amino acids 1-46), CVT11, SAP18, YM8520.08C, YMR159C
Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03818
#3: Protein Ubiquitin-like protein ATG12 / Autophagy-related protein 12


Mass: 10341.172 Da / Num. of mol.: 1 / Fragment: UNP residues 100-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Gene: APG12, ATG12, Atg12(amino acids 100-186), YBR1506, YBR217W
Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38316
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG10000, 0.5M potassium thiocyanate, 0.1M ADA, pH 6.5, 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: Jun 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→42.6 Å / Num. all: 17196 / Num. obs: 17173 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 53.8 Å2 / Rsym value: 0.055 / Net I/σ(I): 9.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.4 % / Num. unique all: 1691 / Rsym value: 0.303 / % 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: 2DYM, 1WZ3

2dym

1wz3


Resolution: 2.6→42.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 167335.04 / 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
Rfree0.258 1679 10 %RANDOM
Rwork0.231 ---
obs0.231 16822 97.9 %-
all-17183 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.3649 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 51.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.38 Å20 Å20 Å2
2---5.38 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 0 27 2895
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.562
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 247 9.5 %
Rwork0.31 2345 -
obs-2592 91.6 %
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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