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- PDB-3vh4: Crystal structure of Atg7CTD-Atg8-MgATP complex -

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Basic information

Entry
Database: PDB / ID: 3vh4
TitleCrystal structure of Atg7CTD-Atg8-MgATP complex
Components
  • Autophagy-related protein 8
  • Ubiquitin-like modifier-activating enzyme ATG7
KeywordsMETAL BINDING PROTEIN/PROTEIN TRANSPORT / autophagy / E1 / zinc binding / METAL BINDING PROTEIN-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


Cvt vesicle membrane / Atg12 activating enzyme activity / Atg8 activating enzyme activity / TBC/RABGAPs / Receptor Mediated Mitophagy / protein modification by small protein conjugation / extrinsic component of phagophore assembly site membrane / regulation of membrane invagination / vacuole-isolation membrane contact site / lipid droplet formation ...Cvt vesicle membrane / Atg12 activating enzyme activity / Atg8 activating enzyme activity / TBC/RABGAPs / Receptor Mediated Mitophagy / protein modification by small protein conjugation / extrinsic component of phagophore assembly site membrane / 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 / protein localization to phagophore assembly site / 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 / Antigen processing: Ubiquitination & Proteasome degradation / autophagosome assembly / autophagosome maturation / regulation of macroautophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / mitophagy / lipid droplet / Neutrophil degranulation / autophagosome / macroautophagy / mitochondrial membrane / autophagy / protein tag activity / membrane fusion / mitochondrion / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Ubiquitin-like modifier-activating enzyme Atg7 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 1 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 2 / Ubiquitin-like modifier-activating enzyme ATG7 N-terminus / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family ...Ubiquitin-like modifier-activating enzyme Atg7 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 1 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 2 / Ubiquitin-like modifier-activating enzyme ATG7 N-terminus / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / NAD(P)-binding Rossmann-like Domain / Ubiquitin-like domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Autophagy-related protein 8 / Ubiquitin-like modifier-activating enzyme ATG7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsNoda, N.N. / Satoo, K. / Inagaki, F.
CitationJournal: Mol.Cell / Year: 2011
Title: Structural basis of Atg8 activation by a homodimeric E1, Atg7.
Authors: Noda, N.N. / Satoo, K. / Fujioka, Y. / Kumeta, H. / Ogura, K. / Nakatogawa, H. / Ohsumi, Y. / Inagaki, F.
History
DepositionAug 23, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Nov 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Ubiquitin-like modifier-activating enzyme ATG7
B: Autophagy-related protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5005
Polymers51,9032
Non-polymers5973
Water00
1
A: Ubiquitin-like modifier-activating enzyme ATG7
B: Autophagy-related protein 8
hetero molecules

A: Ubiquitin-like modifier-activating enzyme ATG7
B: Autophagy-related protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,99910
Polymers103,8054
Non-polymers1,1946
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area13890 Å2
ΔGint-115 kcal/mol
Surface area32010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.282, 69.282, 219.605
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme ATG7 / ATG12-activating enzyme E1 ATG7 / Autophagy-related protein 7 / Cytoplasm to vacuole targeting protein 2


Mass: 38150.859 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP RESIDUES 295-630)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: ATG7, APG7, CVT2, YHR171W / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P38862
#2: Protein Autophagy-related protein 8 / Autophagy-related ubiquitin-like modifier ATG8 / Cytoplasm to vacuole targeting protein 5


Mass: 13751.865 Da / Num. of mol.: 1 / Mutation: K26P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732 / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P38182
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEGMME 5000, 5% tacsimate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 16447 / Num. obs: 16404 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 22.7 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 73.1
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 9.2 / % 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 3VH3

3vh3


Resolution: 2.65→33.04 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 103999 / 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
Rfree0.267 1481 10 %RANDOM
Rwork0.235 ---
all0.238 16368 --
obs0.235 14862 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8378 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 82.6 Å2
Baniso -1Baniso -2Baniso -3
1-18.48 Å20 Å20 Å2
2--18.48 Å20 Å2
3----36.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.65→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 33 0 3317
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_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
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_it2.372
X-RAY DIFFRACTIONc_scbond_it1.752
X-RAY DIFFRACTIONc_scangle_it2.592.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 213 10.6 %
Rwork0.349 1802 -
obs--76.5 %
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
X-RAY DIFFRACTION6ATP2.paramATP3.top

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