1WZ3 - JenaLib

Title :   THE CRYSTAL STRUCTURE OF PLANT ATG12

Authors :   N. N. Suzuki, K. Yoshimoto, Y. Fujioka, Y. Ohsumi, F. Inagaki

Date :   22 Feb 05 (Deposition) - 21 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ubiquitin-Fold, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. N. Suzuki, K. Yoshimoto, Y. Fujioka, Y. Ohsumi, F. Inagaki
The Crystal Structure Of Plant Atg12 And Its Biological Implication In Autophagy.
Autophagy V. 1 119 2005
PubMed-ID: 16874047
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	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:84
 aligned with AT12B_ARATH | Q9LVK3 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:84
                                    19        29        39        49        59        69        79        89    
           AT12B_ARATH   10 QKIVVHLRATGGAPILKQSKFKVSGSDKFANVIDFLRRQLHSDSLFVYVNSAFSPNPDESVIDLYNNFGFDGKLVVNYACSMAW 93
               SCOP domains d1wz3a1 A:10-93 Autophagy-related protein 12b (APG12b)                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..........eeeee....hhhhhhhhhhhhh....eeeeeeee......hhhhhhhhhh....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  1wz3 A 10 QKIVVHLRATGGAPILKQSKFKVSGSDKFANVIDFLRRQLHSDSLFVYVNSAFSPNPDESVIDLYNNFGFDGKLVVNYACSMAW 93
                                    19        29        39        49        59        69        79        89

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with AT12B_ARATH | Q9LVK3 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:84
                                    19        29        39        49        59        69        79        89    
           AT12B_ARATH   10 QKIVVHLRATGGAPILKQSKFKVSGSDKFANVIDFLRRQLHSDSLFVYVNSAFSPNPDESVIDLYNNFGFDGKLVVNYACSMAW 93
               SCOP domains d1wz3b_ B: automated matches                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -APG12-1wz3B01 B:11-93                                                               Pfam domains (1)
           Pfam domains (2) -APG12-1wz3B02 B:11-93                                                               Pfam domains (2)
         Sec.struct. author .eeeeeeeee.........eeeee....hhhhhhhhhhhh.....eeeeeeee......hhhhhhhhhh....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  1wz3 B 10 QKIVVHLRATGGAPILKQSKFKVSGSDKFANVIDFLRRQLHSDSLFVYVNSAFSPNPDESVIDLYNNFGFDGKLVVNYACSMAW 93
                                    19        29        39        49        59        69        79        89

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 (2, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (AT12B_ARATH | Q9LVK3)

molecular function
	GO:0019776	Atg8 ligase activity	Catalysis of the covalent attachment of the ubiquitin-like protein Atg8 to substrate molecules; phosphatidylethanolamine is a known substrate.
	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).
biological process
	GO:0006501	C-terminal protein lipidation	The covalent attachment of a lipid group to the carboxy terminus of a protein.
	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:0044804	autophagy of nucleus	A selective form of autophagy, by which damaged or non-essential parts of the nucleus, or even an entire nucleus is degraded.
	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: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:0034274	Atg12-Atg5-Atg16 complex	A protein complex required for the expansion of the autophagosomal membrane. In budding yeast, this complex consists of Atg12p, Atg5p and Atg16p.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0034045	pre-autophagosomal structure membrane	A cellular membrane associated with the pre-autophagosomal structure.

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