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- PDB-2kzk: Solution structure of alpha-mannosidase binding domain of Atg34 -

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Basic information

Entry
Database: PDB / ID: 2kzk
TitleSolution structure of alpha-mannosidase binding domain of Atg34
ComponentsUncharacterized protein YOL083W
KeywordsPROTEIN TRANSPORT / Selective autophagy / Atg34 / alpha-mannosidase / Atg19
Function / homology
Function and homology information


Cvt complex / protein targeting to vacuole involved in autophagy / phagophore assembly site membrane / protein-containing complex localization / macroautophagy / protein-macromolecule adaptor activity / protein-containing complex assembly / cytosol
Similarity search - Function
Immunoglobulin-like - #2830 / Autophagy protein Atg19/Atg34, C-terminal / Autophagy protein Atg19, Atg8-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Autophagy-related protein 34
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR
Model detailslowest energy, model 1
AuthorsWatanabe, Y. / Noda, N. / Kumeta, H. / Suzuki, K. / Ohsumi, Y. / Inagaki, F.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Selective transport of alpha-mannosidase by autophagic pathways: structural basis for cargo recognition by Atg19 and Atg34.
Authors: Watanabe, Y. / Noda, N.N. / Kumeta, H. / Suzuki, K. / Ohsumi, Y. / Inagaki, F.
History
DepositionJun 18, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 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: Uncharacterized protein YOL083W


Theoretical massNumber of molelcules
Total (without water)11,9581
Polymers11,9581
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein YOL083W


Mass: 11957.606 Da / Num. of mol.: 1 / Fragment: Alpha-mannosidase binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YOL083W, O0957 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12292

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HN(CO)HA
1813D HBHA(CO)NH
1912D 1H-13C HSQC
11013D (H)CCH-TOCSY
11113D 1H-13C NOESY
11213D 1H-15N NOESY
11312D (Hb)Cb(CgCd)Hd
11412D (Hb)Cb(CgCdCe)He

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Sample preparation

DetailsContents: 25 mM sodium phosphate-1, 100 mM sodium chloride-2, 2 mM DTT-3, 0.7 mM [U-99% 13C; U-99% 15N] Alpha-mannosidase binding domain of Atg34-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium phosphate-11
100 mMsodium chloride-21
2 mMDTT-31
0.7 mMAlpha-mannosidase binding domain of Atg34-4[U-99% 13C; U-99% 15N]1
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
VNMRVariancollection
CYANAGuntert, Mumenthaler and Wuthrichrefinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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