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- PDB-3vx8: Crystal structure of Arabidopsis thaliana Atg7NTD-Atg3 complex -

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Basic information

Entry
Database: PDB / ID: 3vx8
TitleCrystal structure of Arabidopsis thaliana Atg7NTD-Atg3 complex
Components
  • Autophagy-related protein 3
  • Ubiquitin-like modifier-activating enzyme atg7
KeywordsLIGASE / E1-E2 complex
Function / homology
Function and homology information


Atg12 activating enzyme activity / Atg8 activating enzyme activity / Atg8-family ligase activity / : / protein modification by small protein conjugation / C-terminal protein lipidation / protein lipidation / leaf senescence / piecemeal microautophagy of the nucleus / autophagy of mitochondrion ...Atg12 activating enzyme activity / Atg8 activating enzyme activity / Atg8-family ligase activity / : / protein modification by small protein conjugation / C-terminal protein lipidation / protein lipidation / leaf senescence / piecemeal microautophagy of the nucleus / autophagy of mitochondrion / cellular response to nitrogen starvation / phagophore assembly site / autophagosome assembly / defense response to fungus / autophagy / protein transport / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like modifier-activating enzyme ATG7 C-terminal domain / Ubiquitin-like modifier-activating enzyme ATG7 N-terminal domain / : / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / 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 ...Ubiquitin-like modifier-activating enzyme ATG7 C-terminal domain / Ubiquitin-like modifier-activating enzyme ATG7 N-terminal domain / : / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / 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 / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Cytidine Deaminase; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 3 / Ubiquitin-like modifier-activating enzyme atg7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.11 Å
AuthorsMatoba, K. / Fujioka, Y. / Noda, N.N.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7.
Authors: Yamaguchi, M. / Matoba, K. / Sawada, R. / Fujioka, Y. / Nakatogawa, H. / Yamamoto, H. / Kobashigawa, Y. / Hoshida, H. / Akada, R. / Ohsumi, Y. / Noda, N.N. / Inagaki, F.
#1: Journal: To be Published
Title: The Autophagy-related Ubiquitin-like Protein Conjugate Atg12-Atg5 Rearranges the Catalytic Site of Atg3 to Enhance Its E2 Activity
Authors: Sakoh-Nakatogawa, M. / Matoba, K. / Asai, E. / Kirisako, H. / Ishii, J. / Noda, N.N. / Inagaki, F. / Nakatogawa, H. / Ohsumi, Y.
History
DepositionSep 11, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
D: Ubiquitin-like modifier-activating enzyme atg7
A: Ubiquitin-like modifier-activating enzyme atg7
B: Autophagy-related protein 3
C: Autophagy-related protein 3


Theoretical massNumber of molelcules
Total (without water)138,0474
Polymers138,0474
Non-polymers00
Water543
1
A: Ubiquitin-like modifier-activating enzyme atg7
B: Autophagy-related protein 3


Theoretical massNumber of molelcules
Total (without water)69,0232
Polymers69,0232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ubiquitin-like modifier-activating enzyme atg7
C: Autophagy-related protein 3


Theoretical massNumber of molelcules
Total (without water)69,0232
Polymers69,0232
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.520, 132.683, 102.805
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme atg7 / ATG12-activating enzyme E1 atg7 / Autophagy-related protein 7 / AtAPG7


Mass: 36012.566 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 7-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ATG7, APG7, At5g45900, K15I22.10 / Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q94CD5
#2: Protein Autophagy-related protein 3 / Autophagy-related E2-like conjugation enzyme ATG3 / AtAPG3 / Protein autophagy 3


Mass: 33010.691 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ATG3, APG3, At5g61500, K11J9.3 / Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0WWQ1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.51 Å3/Da / Density % sol: 50.95 % / Mosaicity: 0.572 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 16% PEG 3350, 100mM Magnesium formate, 20mM Tris-HCl, 2mM DTT, NaCl, pH 8.0, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 15.9 % / Av σ(I) over netI: 16.48 / Number: 368027 / Rmerge(I) obs: 0.158 / Χ2: 3.22 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 23170 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.675010010.07516.58514.7
6.898.6710010.0964.84615
6.026.8910010.123.95415.5
5.476.0210010.1333.65415.7
5.085.4710010.1263.62516
4.785.0810010.1233.67615.9
4.544.7810010.1283.39216
4.344.5410010.143.01216.2
4.184.3410010.1472.71916.3
4.034.1810010.1642.27816.2
3.914.0310010.1792.04716.3
3.793.9110010.2061.94716.3
3.693.7910010.2341.78916.2
3.63.6910010.2711.69816.2
3.523.610010.3211.56516.2
3.453.5299.910.3471.56716.1
3.383.4599.910.4081.4916.1
3.313.3810010.4821.42116
3.263.3199.810.5621.35116.1
3.23.2699.910.6441.34714.8
ReflectionResolution: 3.1→50 Å / Num. obs: 25356 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.162 / Χ2: 2.081 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.155.70.49212411.562199.8
3.15-3.215.80.4312411.562199.6
3.21-3.275.70.3912361.624199.6
3.27-3.345.80.33512621.673199.8
3.34-3.415.70.29212491.743199.9
3.41-3.495.80.25712471.7741100
3.49-3.585.70.23212521.6951100
3.58-3.685.80.2112571.8781100
3.68-3.785.80.19212441.929199.9
3.78-3.915.80.17112581.987199.9
3.91-4.045.70.15712572.062199.9
4.04-4.215.70.14112642.143199.9
4.21-4.45.70.12412652.375199.8
4.4-4.635.70.1212732.3161100
4.63-4.925.70.11312632.363199.7
4.92-5.35.60.11112822.444199.8
5.3-5.835.60.12112662.198199.9
5.83-6.675.60.11713072.296199.9
6.67-8.45.40.09913232.689199.8
8.4-504.80.06913693.467197.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 3.11→34.85 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.835 / WRfactor Rfree: 0.2551 / WRfactor Rwork: 0.2037 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8036 / SU B: 21.357 / SU ML: 0.377 / SU Rfree: 0.4983 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.496 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 1295 5.1 %RANDOM
Rwork0.2261 ---
all0.2288 ---
obs0.2287 24044 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.8 Å2 / Biso mean: 44.9797 Å2 / Biso min: 17.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.11→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7605 0 0 3 7608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197811
X-RAY DIFFRACTIONr_angle_refined_deg0.9741.9610606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9245940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60823.681345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.364151303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6441544
X-RAY DIFFRACTIONr_chiral_restr0.0650.21162
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215902
LS refinement shellResolution: 3.113→3.193 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 88 -
Rwork0.32 1589 -
all-1677 -
obs--91.69 %

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