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(-) Description

Title :  SKICH DOMAIN OF NDP52
 
Authors :  M. Akutsu, N. V. Muhlinen, F. Randow, D. Komander
Date :  28 Jul 12  (Deposition) - 27 Feb 13  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Autophagy Adaptor Protein, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. V. Muhlinen, M. Akutsu, B. J. Ravenhill, A. Foeglein, S. Bloor, T. J. Rutherford, S. M. Freund, D. Komander, F. Randow
Lc3C, Bound Selectively By A Noncanonical Lir Motif In Ndp52, Is Required For Antibacterial Autophagy
Mol. Cell V. 48 329 2012
PubMed-ID: 23022382  |  Reference-DOI: 10.1016/J.MOLCEL.2012.08.024

(-) Compounds

Molecule 1 - CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 21-141
    GeneCALCOCO2, NDP52
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymANTIGEN NUCLEAR DOT 52 KDA PROTEIN, NUCLEAR DOMAIN 10 PROTEIN NDP52, NUCLEAR DOMAIN 10 PROTEIN 52, NUCLEAR DOT PROTEIN 52

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A
Biological Unit 2 (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3VVV)

(-) Sites  (0, 0)

(no "Site" information available for 3VVV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VVV)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:77 -Pro A:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VVV)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:108
 aligned with CACO2_HUMAN | Q13137 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:126
                                    16        26        36        46        56        66        76        86        96       106       116       126      
          CACO2_HUMAN     7 DPPTSAVLLDHCHFSQVIFNSVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWVTLPIDLNNKSAKQQEVQFKAYYLPKDDEYYQFCYVDEDGVVRGASIPFQFRPENEED 132
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..------------..eeee....ee.....eeeeeee..........eeeeee....hhhhh.eeee......------..eeeeehhhhh......eeeeee.....eeee....ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vvv A  19 GP------------SQVIFNSVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWVTLPID------KQQEVQFKAYYLPKDDEYYQFCYVDEDGVVRGASIPFQFRPENEED 132
                             |       -    |   26        36        46        56        66        76   |     -|       96       106       116       126      
                             |           21                                                         80     87                                             
                            20                                                                                                                            

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  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  (0, 0)

(no "SCOP Domain" information available for 3VVV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VVV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VVV)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (CACO2_HUMAN | Q13137)
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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    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:1901098    positive regulation of autophagosome maturation    Any process that activates or increases the frequency, rate or extent of autophagosome maturation.
    GO:0034341    response to interferon-gamma    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon-gamma is also known as type II interferon.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
    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:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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    Leu A:77 - Pro A:78   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        CACO2_HUMAN | Q131372mxp 3vvw 4gxl 4han 4xkl 5aaq

(-) Related Entries Specified in the PDB File

3vvw