1WHD - JenaLib

NMR Structure - manually

NMR Structure - model 1

NMR Structure - all models

collapse

expand

NMR Structure - manually (Jmol Viewer)

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Description

Title :   SOLUTION STRUCTURE OF THE PDZ DOMAIN OF RGS3

Authors :   T. Nakanishi, N. Nemoto, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   28 May 04 (Deposition) - 28 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Regulator Of G-Protein Signaling, Pdz Domain, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nakanishi, N. Nemoto, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Pdz Domain Of Rgs3
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - REGULATOR OF G-PROTEIN SIGNALING 3
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P030714-81
	Expression System Vector Type	:	PLASMID
	Fragment	:	PDZ DOMAIN
	Gene	:	RIKEN CDNA 4930506N09
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	RGS3

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 1WHD)

Sites (0, 0)

(no "Site" information available for 1WHD)

SS Bonds (0, 0)

(no "SS Bond" information available for 1WHD)

Cis Peptide Bonds (1, 20)

NMR Structure

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20	Ser A:36	-	Pro A:37

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1WHD)

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	RGS3_MOUSE	18-95	1	A:18-94

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.13a	ENSMUST00000084521	13a	ENSMUSE00000798656	chr4:62280554-62280821	268	RGS3_MOUSE	1-18	18	1	A:2-18 (gaps)	18
1.15c	ENSMUST00000084521	15c	ENSMUSE00000451224	chr4:62284879-62284960	82	RGS3_MOUSE	19-46	28	1	A:19-46	28
1.16b	ENSMUST00000084521	16b	ENSMUSE00000451215	chr4:62286131-62286236	106	RGS3_MOUSE	46-81	36	1	A:46-81	36
1.17	ENSMUST00000084521	17	ENSMUSE00000451201	chr4:62286776-62287127	352	RGS3_MOUSE	81-198	118	1	A:81-100 (gaps)	25
1.18	ENSMUST00000084521	18	ENSMUSE00000451197	chr4:62287526-62287565	40	RGS3_MOUSE	199-212	14	0	-	-
1.19	ENSMUST00000084521	19	ENSMUSE00000451192	chr4:62292158-62292354	197	RGS3_MOUSE	212-277	66	0	-	-
1.20b	ENSMUST00000084521	20b	ENSMUSE00000451183	chr4:62295480-62295563	84	RGS3_MOUSE	278-305	28	0	-	-
1.21	ENSMUST00000084521	21	ENSMUSE00000451176	chr4:62301751-62301862	112	RGS3_MOUSE	306-343	38	0	-	-
1.22	ENSMUST00000084521	22	ENSMUSE00000451169	chr4:62307718-62307761	44	RGS3_MOUSE	343-357	15	0	-	-
1.23b	ENSMUST00000084521	23b	ENSMUSE00000451165	chr4:62313748-62313870	123	RGS3_MOUSE	358-398	41	0	-	-
1.29d	ENSMUST00000084521	29d	ENSMUSE00000891286	chr4:62350533-62351660	1128	RGS3_MOUSE	399-774	376	0	-	-
1.30a	ENSMUST00000084521	30a	ENSMUSE00000526739	chr4:62358305-62358366	62	RGS3_MOUSE	775-795	21	0	-	-
1.32	ENSMUST00000084521	32	ENSMUSE00000526738	chr4:62361032-62361133	102	RGS3_MOUSE	795-829	35	0	-	-
1.33	ENSMUST00000084521	33	ENSMUSE00000526734	chr4:62361388-62361449	62	RGS3_MOUSE	829-850	22	0	-	-
1.35b	ENSMUST00000084521	35b	ENSMUSE00000526733	chr4:62362068-62362234	167	RGS3_MOUSE	850-905	56	0	-	-
1.36c	ENSMUST00000084521	36c	ENSMUSE00000526731	chr4:62363094-62364052	959	RGS3_MOUSE	906-966	61	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:100
 aligned with RGS3_MOUSE | Q9DC04 from UniProtKB/Swiss-Prot  Length:966

    Alignment length:106
                             1                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99      
           RGS3_MOUSE     - -MNRFNGLCKVCSERRYRQITIRRGKDGFGFTICCDSPVRVQAVDSGGPAERAGLQQLDTVLQLNERPVEHWKCVELAHEIRSCPSEIILLVWRVVPQIKPGPDGG 105
               SCOP domains d1whda_ A: Regul ator of G-protein signaling 3, RGS3                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------PDZ-1whdA01 A:18-92                                                        ------------- Pfam domains
         Sec.struct. author ..............ee-eeeeee.......eee.......eeee.....hhhh.......eeee..ee.....hhhhhhhhhh...eeeeeeee..-----..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------PDZ  PDB: A:18-94 UniProt: 18-95                                              ---------- PROSITE
           Transcript 1 (1) -Exon 1.13a        Exon 1.15c  PDB: A:19-46    ----------------------------------Exon 1.17 UniProt: 81-198 Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.16b  PDB: A:46-81            ------------------------ Transcript 1 (2)
                 1whd A   1 GSSGSSGEGDPENGEK-LQITIRRGKDGFGFTICCDSPVRVQAVDSGGPAERAGLQQLDTVLQLNERPVEHWKCVELAHEIRSCPSEIILLVWRVS-----GPSSG 100
                                    10     | |19        29        39        49        59        69        79        89     |   - |    
                                          16 |                                                                            95    96    
                                            17

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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: PDZ domain (180)

Protein domain: Regulator of G-protein signaling 3, RGS3 (2)

Mouse (Mus musculus) [TaxId: 10090] (1)

d1whda_

CATH Domains (0, 0)

(no "CATH Domain" information available for 1WHD)

Pfam Domains (1, 1)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Mus musculus (Mouse) (26)

PDZ-1whdA01

A:18-92

Gene Ontology (9, 9)

NMR Structure(hide GO term definitions)

Chain A (RGS3_MOUSE | Q9DC04)

molecular function
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0009968	negative regulation of signal transduction	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 1whd)

	Sites
(no "Sites" information available for 1whd)

	Cis Peptide Bonds
		Ser A:36 - Pro A:37	[ RasMol ]

Still Images

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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1whd
		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
	RGS3_MOUSE \| Q9DC04
		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

Analysis Tools

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
	RGS3_MOUSE \| Q9DC04
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 20)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (4, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

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