2ENO - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE PDZ DOMAIN FROM HUMAN SYNAPTOJANIN 2 BINDING PROTEIN

Authors :   H. Endo, M. Yoshida, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   28 Mar 07 (Deposition) - 02 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Mitochondrial Outer Membrane Protein 25, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Endocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Endo, M. Yoshida, F. Hayashi, S. Yokoyama
Solution Structure Of The Pdz Domain From Human Synaptojanin 2 Binding Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SYNAPTOJANIN-2-BINDING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P050509-14
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ DOMAIN
	Gene	:	SYNJ2BP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE PROTEIN SYNTHESIS
	Synonym	:	MITOCHONDRIAL OUTER MEMBRANE PROTEIN 25


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2ENO)

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

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

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051394	V	9	I	SYJ2B_HUMAN	Polymorphism	4356408	A	V	16	I

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	SYJ2B_HUMAN	13-100	1	A:20-107

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000256366	1	ENSE00000807865	chr14:70883807-70883617	191	SYJ2B_HUMAN	1-22	22	1	A:8-29	22
1.2	ENST00000256366	2	ENSE00000658851	chr14:70855323-70855187	137	SYJ2B_HUMAN	22-67	46	1	A:29-74	46
1.3	ENST00000256366	3	ENSE00000658850	chr14:70842488-70842393	96	SYJ2B_HUMAN	68-99	32	1	A:75-106	32
1.4	ENST00000256366	4	ENSE00000807864	chr14:70839848-70833217	6632	SYJ2B_HUMAN	100-145	46	1	A:107-120 (gaps)	18

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:120
 aligned with SYJ2B_HUMAN | P57105 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:124
                                   1                                                                                                                    
                                   | 3        13        23        33        43        53        63        73        83        93       103       113    
          SYJ2B_HUMAN     - -------MNGRVDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQEGDKILSVNGQDLKNLLHQDAVDLFRNAGYAVSLRVQHRLQVQNGPIGHRGEGDPSG 117
               SCOP domains d2enoa_ A: automated matches                                                                                                 SCOP domains
               CATH domains 2enoA00 A:1-120  [code=2.30.42.10, no name defined]                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeeeee.......eeee.............eeeeee...hhhhhh.......eeeee..ee....hhhhhhhhhhhh..eeeeeeeeeee.......----..... Sec.struct. author
                 SAPs(SNPs) ---------------I------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------PDZ  PDB: A:20-107 UniProt: 13-100                                                      ----------------- PROSITE
           Transcript 1 (1) -------Exon 1.1  PDB: A:8-29 ---------------------------------------------Exon 1.3  PDB: A:75-106         Exon 1.4           Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.2  PDB: A:29-74 UniProt: 22-67         -------------------------------------------------- Transcript 1 (2)
                 2eno A   1 GSSGSSGMNGRVDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQEGDKILSVNGQDLKNLLHQDAVDLFRNAGYAVSLRVQHRLQVQNGPIS----GPSSG 120
                                    10        20        30        40        50        60        70        80        90       100       110    |  116    
                                                                                                                                            115  116

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: automated matches (94)

Protein domain: automated matches (94)

Human (Homo sapiens) [TaxId: 9606] (71)

d2enoa_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Pdz3 Domain (191)

Homologous Superfamily: [code=2.30.42.10, no name defined] (191)

Human (Homo sapiens) (120)

2enoA00

A:1-120

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

NMR Structure(hide GO term definitions)

Chain A (SYJ2B_HUMAN | P57105)

molecular function
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0070699	type II activin receptor binding	Interacting selectively and non-covalently with a type II activin receptor.
biological process
	GO:0007266	Rho protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
	GO:0048312	intracellular distribution of mitochondria	Any process that establishes the spatial arrangement of mitochondria within the cell.
	GO:0070373	negative regulation of ERK1 and ERK2 cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0032926	negative regulation of activin receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of any activin receptor signaling pathway.
	GO:0016525	negative regulation of angiogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
	GO:0010596	negative regulation of endothelial cell migration	Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
	GO:0001937	negative regulation of endothelial cell proliferation	Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation.
	GO:1903671	negative regulation of sprouting angiogenesis	Any process that stops, prevents or reduces the frequency, rate or extent of sprouting angiogenesis.
	GO:0032927	positive regulation of activin receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of the activity of any activin receptor signaling pathway.
	GO:2000010	positive regulation of protein localization to cell surface	Any process that activates or increases the frequency, rate or extent of protein localization to the cell surface.
	GO:0002092	positive regulation of receptor internalization	Any process that activates or increases the frequency, rate or extent of receptor internalization.
	GO:0006605	protein targeting	The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
	GO:0008593	regulation of Notch signaling pathway	Any process that modulates the frequency, rate or extent of the Notch signaling pathway.
	GO:0030100	regulation of endocytosis	Any process that modulates the frequency, rate or extent of endocytosis.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0031307	integral component of mitochondrial outer membrane	The component of the mitochondrial outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 2eno)

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

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2eno
		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
	SYJ2B_HUMAN \| P57105
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SYJ2B_HUMAN \| P57105
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SYJ2B_HUMAN \| P57105	:	2jik 2jin

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

Description

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 (1, 1)

PROSITE Motifs (1, 1)

Exons (4, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (23, 23)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File