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(-) Description

Authors :  H. Kumeta, M. Watanabe, H. Nakatogawa, M. Yamaguchi, K. Ogura, W. Adach Y. Fujioka, N. N. Noda, Y. Ohsumi, F. Inagaki
Date :  05 Apr 10  (Deposition) - 12 May 10  (Release) - 30 Jun 10  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Autophagy, Atg8, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  H. Kumeta, M. Watanabe, H. Nakatogawa, M. Yamaguchi, K. Ogura, W. Adachi, Y. Fujioka, N. N. Noda, Y. Ohsumi, F. Inagaki
The Nmr Structure Of The Autophagy-Related Protein Atg8
J. Biomol. Nmr V. 47 237 2010
PubMed-ID: 20428927  |  Reference-DOI: 10.1007/S10858-010-9420-1

(-) Compounds

    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPGEX6P
    Expression System Vector TypeVECTOR
    Organism CommonBAKER'S YEAST
    Organism Taxid4932

 Structural Features

(-) Chains, Units

NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2KWC)

(-) Sites  (0, 0)

(no "Site" information available for 2KWC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KWC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KWC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KWC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2KWC)

(-) Exons   (0, 0)

(no "Exon" information available for 2KWC)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:116
 aligned with ATG8_YEAST | P38182 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
               SCOP domains d2kwca_ A: automated matches                                                                                         SCOP domains
               CATH domains 2kwcA00 A:1-116 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh..eeeeee...............eeee...hhhhhhhhhhhhh........eeee.........hhhhhhhhhh.....eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                                    10        20        30        40        50        60        70        80        90       100       110      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2KWC)

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (ATG8_YEAST | P38182)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0031386    protein tag    A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0000045    autophagosome assembly    The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0000422    autophagy of mitochondrion    The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.
    GO:0034629    cellular protein complex localization    A protein complex localization process that takes place at the cellular level; as a result, a protein complex is transported to, or maintained in, a specific location within a cell.
    GO:0006995    cellular response to nitrogen starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nitrogen.
    GO:0044805    late nucleophagy    A type of nucleophagy, distinct from piecemeal microautophagy of the nucleus (PNM) where the nuclear material is delivered to the vacuole/lysosome for breakdown and recycling later than observed for PNM.
    GO:0061025    membrane fusion    The membrane organization process that joins two lipid bilayers to form a single membrane.
    GO:0034727    piecemeal microautophagy of nucleus    Degradation of a cell nucleus by lysosomal microautophagy.
    GO:0032258    protein localization by the CVT pathway    A cytoplasm to vacuole targeting pathway that uses machinery common with autophagy. The CVT vesicle is formed when the receptor protein, Atg19, binds to the complexes of the target protein (aminopeptidase or alpha-mannosidase homododecamers), forming the Cvt complex. Atg11 binds to Atg9 and transports the CVT complex to the pre-autophagosome (PAS). The phagophore membrane expands around the CVT complex (excluding bulk cytoplasm) forming the CVT vesicle. This pathway is mostly observed in yeast.
    GO:0071211    protein targeting to vacuole involved in autophagy    The process of directing proteins towards the vacuole using signals contained within the protein, occurring as part of autophagy, the process in which cells digest parts of their own cytoplasm.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0061709    reticulophagy    The autophagic process in which parts of the endoplasmic reticulum are loaded into autophagosomes, delivered to the vacuole, and degraded in response to changing cellular conditions.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0033110    Cvt vesicle membrane    Either of the two lipid bilayers surrounding a Cvt vesicle, a vesicle that functions in the cytoplasm-to-vacuole targeting (Cvt) pathway.
    GO:0005776    autophagosome    A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.
    GO:0000421    autophagosome membrane    The lipid bilayer surrounding an autophagosome, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0000329    fungal-type vacuole membrane    The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000407    pre-autophagosomal structure    Punctate structures proximal to the endoplasmic reticulum which are the sites where the Atg machinery assembles upon autophagy induction.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.


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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

        ATG8_YEAST | P381822kq7 2li5 2zpn 3rui 3vh3 3vh4 3vxw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2KWC)