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- PDB-3t7g: Atg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture... -

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Basic information

Entry
Database: PDB / ID: 3t7g
TitleAtg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture and mechanism in the autophagy pathway
Components
  • Autophagy-related protein 3
  • Ubiquitin-like modifier-activating enzyme ATG7
KeywordsLIGASE / Atg7 / Atg3 / autophagy / E1
Function / homology
Function and homology information


Atg12 activating enzyme activity / Atg8 activating enzyme activity / Atg8-family ligase activity / phagophore / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / C-terminal protein lipidation / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy ...Atg12 activating enzyme activity / Atg8 activating enzyme activity / Atg8-family ligase activity / phagophore / extrinsic component of phagophore assembly site membrane / protein modification by small protein conjugation / C-terminal protein lipidation / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / phagophore assembly site / protein targeting to membrane / autophagosome assembly / Neutrophil degranulation / macroautophagy / autophagy / protein transport / mitochondrion / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / 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 / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme ...: / 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 / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme ATG7 / Autophagy-related protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsTaherbhoy, A.M. / Tait, S.W. / Kaiser, S.E. / Williams, A.H. / Deng, A. / Nourse, A. / Hammel, M. / Kurinov, I. / Rock, C.O. / Green, D.R. / Schulman, B.A.
CitationJournal: Mol.Cell / Year: 2011
Title: Atg8 transfer from atg7 to atg3: a distinctive e1-e2 architecture and mechanism in the autophagy pathway.
Authors: Taherbhoy, A.M. / Tait, S.W. / Kaiser, S.E. / Williams, A.H. / Deng, A. / Nourse, A. / Hammel, M. / Kurinov, I. / Rock, C.O. / Green, D.R. / Schulman, B.A.
History
DepositionJul 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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: Ubiquitin-like modifier-activating enzyme ATG7
B: Ubiquitin-like modifier-activating enzyme ATG7
D: Autophagy-related protein 3
C: Autophagy-related protein 3


Theoretical massNumber of molelcules
Total (without water)70,9174
Polymers70,9174
Non-polymers00
Water3,423190
1
A: Ubiquitin-like modifier-activating enzyme ATG7
C: Autophagy-related protein 3


Theoretical massNumber of molelcules
Total (without water)35,4582
Polymers35,4582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-like modifier-activating enzyme ATG7
D: Autophagy-related protein 3


Theoretical massNumber of molelcules
Total (without water)35,4582
Polymers35,4582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.135, 99.429, 71.502
Angle α, β, γ (deg.)90.00, 113.13, 90.00
Int Tables number5
Space group name H-MC121

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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: 33422.285 Da / Num. of mol.: 2 / Fragment: NTD, UNP residues 1-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATG7, APG7, CVT2, YHR171W / Production host: Escherichia coli (E. coli) / References: UniProt: P38862
#2: Protein/peptide Autophagy-related protein 3 / Autophagy-related E2-like conjugation enzyme ATG3


Mass: 2036.193 Da / Num. of mol.: 2 / Fragment: FR, UNP residues 128-144 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40344
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.8M ammonium sulfate, 0.1M Bis-Tris pH 5.5, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 58224

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T7F

3t7f


Resolution: 2.08→33.212 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 2944 5.07 %
Rwork0.1817 --
obs0.1829 58121 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.027 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.6167 Å2-0 Å21.1302 Å2
2---2.5522 Å2-0 Å2
3---7.1689 Å2
Refinement stepCycle: LAST / Resolution: 2.08→33.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4550 0 0 190 4740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084683
X-RAY DIFFRACTIONf_angle_d1.0336379
X-RAY DIFFRACTIONf_dihedral_angle_d12.421665
X-RAY DIFFRACTIONf_chiral_restr0.071738
X-RAY DIFFRACTIONf_plane_restr0.005817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0801-2.11420.27111080.23952149X-RAY DIFFRACTION80
2.1142-2.15060.22371460.2112607X-RAY DIFFRACTION100
2.1506-2.18970.23971450.20872589X-RAY DIFFRACTION100
2.1897-2.23180.26941650.20812662X-RAY DIFFRACTION100
2.2318-2.27740.22461440.20542611X-RAY DIFFRACTION100
2.2774-2.32690.20821530.19192676X-RAY DIFFRACTION100
2.3269-2.3810.1977950.19822675X-RAY DIFFRACTION100
2.381-2.44050.23791430.20142610X-RAY DIFFRACTION100
2.4405-2.50650.23121410.19922657X-RAY DIFFRACTION100
2.5065-2.58020.2381510.19862638X-RAY DIFFRACTION100
2.5802-2.66340.24271460.22645X-RAY DIFFRACTION100
2.6634-2.75860.23581490.21372647X-RAY DIFFRACTION100
2.7586-2.8690.23031280.19292650X-RAY DIFFRACTION100
2.869-2.99950.21711440.18292654X-RAY DIFFRACTION100
2.9995-3.15750.22151370.19312663X-RAY DIFFRACTION100
3.1575-3.35520.20171360.18212651X-RAY DIFFRACTION100
3.3552-3.61390.21171360.17132666X-RAY DIFFRACTION100
3.6139-3.97710.1941390.15832688X-RAY DIFFRACTION100
3.9771-4.55130.16221510.14852657X-RAY DIFFRACTION100
4.5513-5.72940.18051560.16262653X-RAY DIFFRACTION100
5.7294-33.21620.20741310.20072729X-RAY DIFFRACTION99
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)
13.4051-0.21050.19731.89390.16731.53290.08820.12770.21750.0178-0.0093-0.23030.023-0.1701-0.0810.2229-0.00170.01660.17290.04490.16435.7361-39.264423.2275
23.7009-2.4641-0.01915.05480.19962.52650.6720.91420.5718-1.204-0.5737-0.88080.02840.2931-0.06280.56890.21660.21810.45090.14590.534832.167-63.29515.5551
35.09280.2075-1.64956.2123-1.3395.9501-0.4771-0.05150.2949-0.2361-0.395-0.66520.18550.82980.84730.4288-0.00330.1460.57480.06770.87929.5606-35.126218.7285
41.24013.55350.76931.99932.20320.47780.5520.123-1.79620.63-0.0304-0.84230.55150.307-0.39490.6070.1177-0.18170.4448-0.0831.188139.0236-59.483637.6246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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