2YT7 - JenaLib

Title :   SOLUTION STRUCTURE OF THE PDZ DOMAIN OF AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY A MEMBER 3

Authors :   W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Tarada, M. Seiki, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   05 Apr 07 (Deposition) - 15 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Nmr, Pdz Domain, Amyloid Beta A4 Precursor Protein-Binding Family A Member 3, Neuron-Specific X11L2 Protein, Neuronal Munc18-1-Interacting Protein 3, Mint-3, Adapter Protein X11Gamma, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Tarada, M. Seiki, S. Yokoyama
Solution Structure Of The Pdz Domain Of Amyloid Beta A4 Precursor Protein-Binding Family A Member 3
To Be Published
PubMed: search
(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 (1, 1)

Exons (0, 0)

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
	(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:101
 aligned with APBA3_HUMAN | O96018 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:113
                                   380       390       400       410       420       430       440       450       460       470       480   
          APBA3_HUMAN   371 PSPGACHLHNGDLDHFSNSDNCREVHLEKRRGEGLGVALVESGWGSLLPTAVIANLLHGGPAERSGALSIGDRLTAINGTSLVGLPLAACQAAVRETKSQTSVTLSIVHCPPV 483
               SCOP domains d2yt            7a_ A: automated matches                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------PDZ-2yt7A01 A:12-96                                                                  ----- Pfam domains
         Sec.struct. author ....------------.....eeeeeee........eeeee.........eeeeee......hhh.......eeeee.........hhhhhhhhhh.....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------PDZ  PDB: A:12-97 UniProt: 394-479                                                    ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2yt7 A   1 GSSG------------SSGDNCREVHLEKRRGEGLGVALVESGWGSLLPTAVIANLLHGGPAERSGALSIGDRLTAINGTSLVGLPLAACQAAVRETKSQTSVTLSIVHCPPV 101
                               |     -      |  8        18        28        38        48        58        68        78        88        98   
                               4            5

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)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (13, 13)

NMR Structure(hide GO term definitions)

Chain A (APBA3_HUMAN | O96018)

molecular function
	GO:0001540	amyloid-beta binding	Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0004857	enzyme inhibitor activity	Binds to and stops, prevents or reduces the activity of an enzyme.
	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:0007268	chemical synaptic transmission	The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
	GO:0001701	in utero embryonic development	The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
	GO:0043086	negative regulation of catalytic activity	Any process that stops or reduces the activity of an enzyme.
	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:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Visualization

Interactive Views

NMR Structure
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2yt7)

	Sites
(no "Sites" information available for 2yt7)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2yt7)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2yt7
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	APBA3_HUMAN \| O96018
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description