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- PDB-2kq7: Solution structure of the Autophagy-Related Protein Atg8 -

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Basic information

Entry
Database: PDB / ID: 2kq7
TitleSolution structure of the Autophagy-Related Protein Atg8
ComponentsAutophagy-related protein 8
KeywordsPROTEIN TRANSPORT / Autophagy / ubiquitin fold / Cytoplasmic vesicle / Lipoprotein / Membrane / Transport / Ubl conjugation pathway / Vacuole
Function / homology
Function and homology information


Cvt vesicle membrane / TBC/RABGAPs / Receptor Mediated Mitophagy / 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 ...Cvt vesicle membrane / TBC/RABGAPs / Receptor Mediated Mitophagy / 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 / protein-containing complex localization / phosphatidylethanolamine binding / fungal-type vacuole membrane / phagophore assembly site / cellular response to nitrogen starvation / reticulophagy / autophagosome membrane / autophagosome assembly / autophagosome maturation / regulation of macroautophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / mitophagy / lipid droplet / autophagosome / mitochondrial membrane / autophagy / protein tag activity / membrane fusion / cytosol / cytoplasm
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsSchwarten, M. / Stoldt, M. / Mohrluder, J. / Willbold, D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Solution structure of Atg8 reveals conformational polymorphism of the N-terminal domain
Authors: Schwarten, M. / Stoldt, M. / Mohrluder, J. / Willbold, D.
History
DepositionOct 29, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autophagy-related protein 8


Theoretical massNumber of molelcules
Total (without water)13,7931
Polymers13,7931
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)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 13792.940 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATG8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Rosetta / References: UniProt: P38182

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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
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HNHA
1713D (H)CCH-COSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11021D 1H

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Sample preparation

Details
Solution-IDContentsSolvent system
120mM sodium phosphate-1, 150mM sodium chloride-2, 5mM DTT-3, 1mM EDTA-4, 0.05% sodium azide-5, 0.5mM [U-13C; U-15N] Atg8-6, 93% H2O/7% D2O93% H2O/7% D2O
220mM sodium phosphate-7, 150mM sodium chloride-8, 5mM DTT-9, 1mM EDTA-10, 0.05% sodium azide-11, 0.5mM [U-13C; U-15N] Atg8-12, 1mM DSS-13, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate-11
150 mMsodium chloride-21
5 mMDTT-31
1 mMEDTA-41
0.05 %sodium azide-51
0.5 mMAtg8-6[U-13C; U-15N]1
20 mMsodium phosphate-72
150 mMsodium chloride-82
5 mMDTT-92
1 mMEDTA-102
0.05 %sodium azide-112
0.5 mMAtg8-12[U-13C; U-15N]2
1 mMDSS-132
Sample conditionspH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS8001
Varian Unity_INOVAVarianUnity_INOVA6002

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKellerchemical shift assignment
CYANAGuntert, Braun and Wuthrichstructure solution
CYANAGuntert, Braun and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15 / Representative conformer: 1

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