1K7B - JenaLib

Title :   NMR SOLUTION STRUCTURE OF STVA47, THE VIRAL-BINDING DOMAIN OF TVA

Authors :   M. Tonelli, R. J. Peters, T. L. James, D. A. Agard

Date :   18 Oct 01 (Deposition) - 19 Dec 01 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Beta Hairpin, 3-10 Helix, Calcium Binding, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Tonelli, R. J. Peters, T. L. James, D. A. Agard
The Solution Structure Of The Viral Binding Domain Of Tva, The Cellular Receptor For Subgroup A Avian Leukosis And Sarcoma Virus.
Febs Lett. V. 509 161 2001
PubMed-ID: 11768384 | Reference-DOI: 10.1016/S0014-5793(01)03086-1
(for further references see the PDB file header)

Compounds

Molecule 1 - SUBGROUP A ROUS SARCOMA VIRUS RECEPTOR PG800 AND PG950
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MBP-FUSION PMAL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SOLUBLE EXTRACELLULAR VIRAL-BINDING DOMAIN
	Organism Common	:	COMMON QUAIL
	Organism Scientific	:	COTURNIX COTURNIX
	Organism Taxid	:	9091
	Synonym	:	LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (3, 3)

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:42
 aligned with RSVR_COTJA | P98162 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:43
                                    37        47        57        67   
            RSVR_COTJA   28 SRCPPGQFRCSEPPGAHGECYPQDWLCDGHPDCDDGRDEWGCG 70
               SCOP domains d 1k7ba_ A: soluble Tva ectodomain, sTva47  SCOP domains
               CATH domains 1 k7bA00 A:10-51                            CATH domains
               Pfam domains --Ldl_recept_a-1k7bA01 A:11-50            - Pfam domains
         Sec.struct. author .-....ee............ee.hhh............hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE -LDLRA_2  PDB: A:11-51 UniProt: 29-70       PROSITE
                 Transcript ------------------------------------------- Transcript
                  1k7b A 10 S-CPPGQFRCSEPPGAHGECYPQDWLCDGHPDCDDGRDEWGCG 51
                            | |     18        28        38        48   
                            | |                                        
                           10 |                                        
                             11

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 (1, 1)

Pfam Domains (1, 1)

Gene Ontology (2, 2)

NMR Structure(hide GO term definitions)

Chain A (RSVR_COTJA | P98162)

cellular component
	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:0016020		membrane		A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 1k7b)

	Sites
(no "Sites" information available for 1k7b)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1k7b)

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
	1k7b
		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
	RSVR_COTJA \| P98162
		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
	RSVR_COTJA \| P98162
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description