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- PDB-2kwc: The NMR structure of the autophagy-related protein Atg8 -

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Basic information

Entry
Database: PDB / ID: 2kwc
TitleThe NMR structure of the autophagy-related protein Atg8
ComponentsAutophagy-related protein 8
KeywordsPROTEIN TRANSPORT / Autophagy / Atg8
Function / homology
Function and homology information


Cvt vesicle membrane / TBC/RABGAPs / Receptor Mediated Mitophagy / regulation of membrane invagination / 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 ...Cvt vesicle membrane / TBC/RABGAPs / Receptor Mediated Mitophagy / regulation of membrane invagination / 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 / autophagosome assembly / autophagosome / regulation of macroautophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / mitochondrial membrane / macroautophagy / protein tag activity / autophagy / protein transport / 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
AuthorsKumeta, H. / Watanabe, M. / Nakatogawa, H. / Yamaguchi, M. / Ogura, K. / Adachi, W. / Fujioka, Y. / Noda, N.N. / Ohsumi, Y. / Inagaki, F.
CitationJournal: J.Biomol.Nmr / Year: 2010
Title: The NMR structure of the autophagy-related protein Atg8
Authors: Kumeta, H. / Watanabe, M. / Nakatogawa, H. / Yamaguchi, M. / Ogura, K. / Adachi, W. / Fujioka, Y. / Noda, N.N. / Ohsumi, Y. / Inagaki, F.
History
DepositionApr 5, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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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)13,4601
Polymers13,4601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 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: 13459.552 Da / Num. of mol.: 1 / Mutation: K26P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / 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 HN(CO)CA
1513D HNCA
1613D HBHA(CO)NH
1713D HN(CA)HA
1813D C(CO)NH
1913D (H)CCH-TOCSY
11013D CCH-TOCSY
11112D (HB)CB(CGCD)HD
11212D (HB)CB(CGCDCE)HE
11313D 1H-15N NOESY
11413D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.6mM [U-99% 13C; U-99% 15N] Atg8 K26P; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.6 mM / Component: Atg8 K26P-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 170 / pH: 6.8 / Pressure: ambient / Temperature: 297 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS2007.068.09.07Cornilescu, Delaglio and Baxdata analysis
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: 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: 20 / Representative conformer: 1

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