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- PDB-5yec: Crystal structure of Atg7CTD-Atg8-MgATP complex in form II -

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Basic information

Entry
Database: PDB / ID: 5yec
TitleCrystal structure of Atg7CTD-Atg8-MgATP complex in form II
Components
  • Autophagy-related protein 8
  • Ubiquitin-like modifier-activating enzyme ATG7
KeywordsPROTEIN TRANSPORT/METAL BINDING PROTEIN / Autophagy / E1 enzyme / Ubiquitin-like protein / METAL BINDING PROTEIN / PROTEIN TRANSPORT-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


Cvt vesicle membrane / Atg12 activating enzyme activity / Atg8 activating enzyme activity / TBC/RABGAPs / Receptor Mediated Mitophagy / extrinsic component of phagophore assembly site membrane / regulation of membrane invagination / protein modification by small protein conjugation / lipid droplet formation / vacuole-isolation membrane contact site ...Cvt vesicle membrane / Atg12 activating enzyme activity / Atg8 activating enzyme activity / TBC/RABGAPs / Receptor Mediated Mitophagy / extrinsic component of phagophore assembly site membrane / regulation of membrane invagination / protein modification by small protein conjugation / lipid droplet formation / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / protein-containing complex localization / phosphatidylethanolamine binding / fungal-type vacuole membrane / phagophore assembly site / reticulophagy / cellular response to nitrogen starvation / autophagy of mitochondrion / Antigen processing: Ubiquitination & Proteasome degradation / autophagosome membrane / autophagosome maturation / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / regulation of macroautophagy / Neutrophil degranulation / autophagosome / lipid droplet / macroautophagy / mitochondrial membrane / autophagy / protein tag activity / membrane fusion / mitochondrion / identical protein binding / membrane / cytosol / cytoplasm
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: 2.147 Å
AuthorsYamaguchi, M. / Satoo, K. / Noda, N.N.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Atg7 Activates an Autophagy-Essential Ubiquitin-like Protein Atg8 through Multi-Step Recognition.
Authors: Yamaguchi, M. / Satoo, K. / Suzuki, H. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F. / Noda, N.N.
History
DepositionSep 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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
C: Ubiquitin-like modifier-activating enzyme ATG7
D: Autophagy-related protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,99910
Polymers103,8054
Non-polymers1,1946
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-85 kcal/mol
Surface area33560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.995, 138.995, 134.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 4 molecules ACBD

#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.: 2 / Fragment: UNP residues 295-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ATG7, APG7, CVT2, YHR171W / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 2 / Mutation: K26P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38182

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Non-polymers , 4 types, 181 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% polyethylene glycol monoethyl ether 5000, 0.1M HEPES, 5% tacsimate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→79.42 Å / Num. obs: 69987 / % possible obs: 97.1 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 10
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 1.3 / % possible all: 82.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.147→49.142 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2186 7018 10.04 %
Rwork0.1998 --
obs0.2017 69903 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.147→49.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6162 0 66 175 6403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036355
X-RAY DIFFRACTIONf_angle_d0.6798656
X-RAY DIFFRACTIONf_dihedral_angle_d15.0343811
X-RAY DIFFRACTIONf_chiral_restr0.0421014
X-RAY DIFFRACTIONf_plane_restr0.0041090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1475-2.17190.3381830.3271569X-RAY DIFFRACTION74
2.1719-2.19740.33592030.31781688X-RAY DIFFRACTION80
2.1974-2.22420.3471950.30241813X-RAY DIFFRACTION85
2.2242-2.25240.33251920.28581845X-RAY DIFFRACTION86
2.2524-2.2820.312230.26641922X-RAY DIFFRACTION90
2.282-2.31330.27212230.25342032X-RAY DIFFRACTION95
2.3133-2.34630.26952480.24952084X-RAY DIFFRACTION99
2.3463-2.38130.27232430.24722131X-RAY DIFFRACTION100
2.3813-2.41850.25652480.24022130X-RAY DIFFRACTION100
2.4185-2.45820.2572000.21662163X-RAY DIFFRACTION100
2.4582-2.50060.24852350.21642135X-RAY DIFFRACTION100
2.5006-2.5460.25162180.21512169X-RAY DIFFRACTION100
2.546-2.5950.25792460.22192137X-RAY DIFFRACTION100
2.595-2.6480.23692380.21362154X-RAY DIFFRACTION100
2.648-2.70560.25172290.22622144X-RAY DIFFRACTION100
2.7056-2.76850.24392380.21222160X-RAY DIFFRACTION100
2.7685-2.83770.23572540.21432133X-RAY DIFFRACTION100
2.8377-2.91440.24352560.20942133X-RAY DIFFRACTION100
2.9144-3.00020.24222440.20912154X-RAY DIFFRACTION100
3.0002-3.0970.23692550.22072129X-RAY DIFFRACTION100
3.097-3.20770.23132390.21592166X-RAY DIFFRACTION100
3.2077-3.33610.26432730.21942135X-RAY DIFFRACTION100
3.3361-3.48790.20542450.19972167X-RAY DIFFRACTION100
3.4879-3.67170.20062350.18312188X-RAY DIFFRACTION100
3.6717-3.90170.20112510.1752169X-RAY DIFFRACTION100
3.9017-4.20280.18962390.17232208X-RAY DIFFRACTION100
4.2028-4.62540.18892290.15452217X-RAY DIFFRACTION100
4.6254-5.2940.17622420.1742217X-RAY DIFFRACTION100
5.294-6.66730.222340.20332273X-RAY DIFFRACTION100
6.6673-49.1550.18752600.19692320X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.29540.45721.27957.0648-1.21999.1028-0.1017-0.38140.21460.31410.39390.36460.2724-0.3865-0.20430.5161-0.08610.11170.44490.07110.4082-15.8774-43.4926-15.2853
23.3344-0.4248-0.6461.7940.552.9504-0.0129-0.31020.28780.03310.0807-0.31020.20870.6229-0.0850.3310.05680.06190.4399-0.01720.36916.0297-35.5512-27.0855
33.9006-0.6299-0.53072.2581-0.06283.5178-0.03620.6172-0.0287-0.5840.1157-0.3090.30640.0911-0.07390.4318-0.01350.11670.4304-0.02190.34-5.561-37.0874-39.5152
43.5286-0.7143-1.7611.4408-0.03472.74520.03570.55230.169-0.4441-0.0872-0.34860.29490.31340.01480.4420.030.12450.5389-0.00220.43368.9314-38.2443-51.313
53.8181-0.38223.30331.0673-0.31832.8573-0.89580.10220.3983-0.711.25090.4060.6561-1.2465-0.33352.0137-0.1495-0.71531.46610.37551.1123-9.4145-33.2699-85.364
66.00453.2541-1.16118.90790.15082.0183-1.21990.8137-0.6259-1.11931.51050.12422.5591.5239-0.35122.0174-0.00940.131.2941-0.08970.7059-2.8044-43.74-83.2788
72.03063.23321.85562.0246-3.03874.5025-0.75950.44690.649-1.27050.3393-0.00170.56730.41360.32791.3030.0843-0.06670.71220.11390.7166-0.5402-38.8162-73.75
86.6585-4.46330.06392.00422.75714.6039-0.458-0.69321.5053-1.79540.28350.7461-0.8933-0.10950.10631.21580.0373-0.07360.71860.09641.4979-6.4968-23.1601-74.2651
94.91120.859-1.43027.6808-4.57649.1921-0.80360.48410.4307-1.88950.0201-0.01031.04330.85470.75150.87940.0575-0.00840.79720.13920.56521.56-37.7013-68.8037
107.69090.42480.3832.0076-1.30826.9932-0.9077-0.47871.0037-0.92610.80060.1558-0.63820.56570.10010.7293-0.0672-0.09310.8492-0.01330.69150.3471-28.5363-65.135
113.7992-4.6584-1.50725.72592.30182.00130.1054-0.10460.3733-0.21370.10970.1521-1.3171-0.1085-0.17721.48280.1752-0.27990.7658-0.13461.081-5.7935-23.1617-64.0196
122.0147-4.30597.25472.0195-1.21582.0139-0.9297-0.50351.1182-1.06710.54871.93630.141-1.60940.39920.84860.0849-0.33521.07580.06831.1246-10.4084-36.5033-62.2398
132.68191.50832.45573.07443.23377.1183-0.60840.35020.1606-1.50940.56820.67140.372-0.34860.12031.12660.0963-0.19090.7760.11450.7147-8.8692-43.08-71.6693
142.0075-0.5497-0.78581.8265-3.79238.2250.17560.13471.0027-1.41480.61650.49120.61040.2317-0.80861.07920.0311-0.35820.6953-0.08560.8754-9.3581-30.659-71.0209
155.1046-0.5666-1.83551.93011.07062.5728-0.19230.26690.1041-0.54-0.1751-1.441-0.22890.8310.32840.8091-0.11470.37820.63410.16471.1193-1.5362-8.2278-35.2717
163.8674-1.0634-0.56941.50240.15793.54140.0304-0.30380.73630.13720.1637-0.2134-0.44750.11-0.19170.3756-0.03650.09590.2794-0.11070.4853-17.8151-17.2794-14.7951
177.2692-4.49790.7734.1243-2.16113.3780.1406-0.220.2837-0.00690.06140.4264-0.4097-0.7414-0.16130.35880.04630.09210.48810.01650.4183-29.0835-20.7904-28.8821
185.4173-1.83810.86696.41661.54063.4276-0.04570.43190.3489-0.19620.07640.0974-0.2171-0.3894-0.07640.30620.0230.1150.35180.02220.3632-19.4801-20.9301-31.9517
193.4989-0.5291-0.58652.20410.33573.0906-0.04750.40660.4707-0.04480.00520.5658-0.2604-1.30980.02720.40460.06040.08850.73560.13420.5397-39.7656-18.4549-23.5836
201.9989.7849-4.66377.0708-3.37431.60350.7019-1.6888-1.94910.1354-0.59561.75392.3942-3.9498-0.11931.627-1.38-0.48692.9481-0.66971.3429-60.828-29.9575-53.8544
215.19882.91231.80982.00581.41016.1008-1.15450.74980.2468-1.39410.45621.10260.0566-0.59940.56521.1135-0.3614-0.10961.80690.24471.2533-60.24-20.5695-45.5357
222.0383-1.94451.725.5572-2.38861.60920.5352-0.639-0.14650.2744-0.50022.33261.0123-0.37780.07581.2794-0.21590.06961.1989-0.18131.6521-50.2123-39.2965-45.2499
233.89221.2164.27189.77450.87459.0453-0.6671.0479-0.4501-1.1331.84291.86821.2423-1.7107-1.25840.8624-0.4117-0.01111.55850.19430.9509-49.0519-27.4904-36.2629
242.0299-2.43523.14976.22526.3839.6107-1.3142.7022-0.72-0.92061.02010.73290.30650.54690.38021.2046-0.4618-0.16191.65240.06050.9934-42.5726-30.2796-46.3397
258.71321.9896.36061.88462.4469.3359-0.55262.3413-0.1464-0.69960.52470.73440.6227-1.5502-0.01550.8721-0.27340.04431.78930.06790.8878-48.3195-21.2817-46.4811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 296 through 313 )
2X-RAY DIFFRACTION2chain 'A' and (resid 314 through 452 )
3X-RAY DIFFRACTION3chain 'A' and (resid 453 through 552 )
4X-RAY DIFFRACTION4chain 'A' and (resid 553 through 616 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 10 )
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 35 )
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 47 )
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 56 )
10X-RAY DIFFRACTION10chain 'B' and (resid 57 through 67 )
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 79 )
12X-RAY DIFFRACTION12chain 'B' and (resid 80 through 90 )
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 104 )
14X-RAY DIFFRACTION14chain 'B' and (resid 105 through 111 )
15X-RAY DIFFRACTION15chain 'C' and (resid 302 through 319 )
16X-RAY DIFFRACTION16chain 'C' and (resid 320 through 462 )
17X-RAY DIFFRACTION17chain 'C' and (resid 463 through 492 )
18X-RAY DIFFRACTION18chain 'C' and (resid 493 through 552 )
19X-RAY DIFFRACTION19chain 'C' and (resid 553 through 615 )
20X-RAY DIFFRACTION20chain 'D' and (resid 4 through 10 )
21X-RAY DIFFRACTION21chain 'D' and (resid 11 through 35 )
22X-RAY DIFFRACTION22chain 'D' and (resid 36 through 47 )
23X-RAY DIFFRACTION23chain 'D' and (resid 48 through 67 )
24X-RAY DIFFRACTION24chain 'D' and (resid 68 through 84 )
25X-RAY DIFFRACTION25chain 'D' and (resid 85 through 109 )

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