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- PDB-2li5: NMR structure of Atg8-Atg7C30 complex -

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Basic information

Entry
Database: PDB / ID: 2li5
TitleNMR structure of Atg8-Atg7C30 complex
Components
  • Autophagy-related protein 8
  • Ubiquitin-like modifier-activating enzyme ATG7
KeywordsPROTEIN TRANSPORT / ATG8 / Autophagy / ubiquitin like
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 / C-terminal protein lipidation / 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 / C-terminal protein lipidation / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / phosphatidylethanolamine binding / protein-containing complex localization / fungal-type vacuole membrane / phagophore assembly site / reticulophagy / autophagosome membrane / Antigen processing: Ubiquitination & Proteasome degradation / autophagosome maturation / autophagosome assembly / autophagosome / regulation of macroautophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / Neutrophil degranulation / mitochondrial membrane / macroautophagy / autophagy / protein tag activity / membrane fusion / ubiquitin protein ligase binding / 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 / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold ...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 / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 8 / Ubiquitin-like modifier-activating enzyme ATG7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsKumeta, H. / Satoo, K. / Noda, N.N. / Fujioka, Y. / Ogura, K. / Nakatogawa, H. / Ohsumi, Y. / 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: BMRB / Processing site: PDBJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autophagy-related protein 8
B: Ubiquitin-like modifier-activating enzyme ATG7


Theoretical massNumber of molelcules
Total (without water)17,4462
Polymers17,4462
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Autophagy-related protein 8 / Atg8 / Autophagy-related ubiquitin-like modifier ATG8 / Cytoplasm to vacuole targeting protein 5


Mass: 13597.699 Da / Num. of mol.: 1 / Mutation: K26P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732 / Production host: Aspergillus niger (mold) / References: UniProt: P38182
#2: Protein/peptide Ubiquitin-like modifier-activating enzyme ATG7 / ATG7C30 / ATG12-activating enzyme E1 ATG7 / Autophagy-related protein 7 / Cytoplasm to vacuole ...ATG7C30 / ATG12-activating enzyme E1 ATG7 / Autophagy-related protein 7 / Cytoplasm to vacuole targeting protein 2


Mass: 3848.143 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 601-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ATG7, APG7, CVT2, YHR171W / Production host: Escherichia coli (E. coli) / References: UniProt: P38862

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D 1H-15N NOESY
1413D 1H-13C NOESY aliphatic
1513D (H)CCH-TOCSY aliphatic
1612D (HB)CB(CGCD)HD
1712D 1H-13C HSQC aromatic
1813D HNCA
1913D HNCO
11013D 1H-13C NOESY aromatic
11113D CBCA(CO)NH
11222D 1H-15N HSQC
11323D HNCO
11423D HN(CA)CB
11523D HN(CA)CB
11623D 1H-15N NOESY
11723D C(CO)NH
11822D 1H-13C HSQC aliphatic
11923D 1H-13C NOESY aliphatic
12022D 1H-13C HSQC aromatic
12123D (H)CCH-TOCSY aliphatic
12213D (H)CCH-TOCSY aromatic
12323D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-99% 13C; U-99% 15N] Atg8K26P-1, 2.0 mM ATG7C30-2, 20 mM sodium phosphate-3, 150 mM sodium chloride-4, 5 mM DTT-5, 5 mM DSS-6, 0.02 % sodium azide-7, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-99% 13C; U-99% 15N] ATG7C30-8, 1.25 mM Atg8K26P-9, 20 mM sodium phosphate-10, 150 mM sodium chloride-11, 5 mM DTT-12, 5 mM DSS-13, 0.02 % sodium azide-14, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMAtg8K26P-1[U-99% 13C; U-99% 15N]1
2.0 mMATG7C30-21
20 mMsodium phosphate-31
150 mMsodium chloride-41
5 mMDTT-51
5 mMDSS-61
0.02 %sodium azide-71
0.5 mMATG7C30-8[U-99% 13C; U-99% 15N]2
1.25 mMAtg8K26P-92
20 mMsodium phosphate-102
150 mMsodium chloride-112
5 mMDTT-122
5 mMDSS-132
0.02 %sodium azide-142
Sample conditionsIonic strength: 170 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA5004

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe5.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
Sparky3.113Goddardrefinement
TALOS+1.01Chen, Cornilescu, Delaglio, Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 19 / Representative conformer: 1

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