1XVJ - JenaLib

Title :   CRYSTAL STRUCTURE OF RAT ALPHA-PARVALBUMIN D94S/G98E MUTANT

Authors :   J. J. Tanner, S. Agah, Y. H. Lee, M. T. Henzl

Date :   28 Oct 04 (Deposition) - 20 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Parvalbumin, Calcium-Binding Protein, Ef Hand Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Tanner, S. Agah, Y. H. Lee, M. T. Henzl
Crystal Structure Of The D94S/G98E Variant Of Rat Alpha-Parvalbumin. An Explanation For The Reduced Divalent Ion Affinity.
Biochemistry V. 44 10966 2005
PubMed-ID: 16101280 | Reference-DOI: 10.1021/BI050770T
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

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:109
 aligned with PRVA_RAT | P02625 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:109
                                    11        21        31        41        51        61        71        81        91       101         
             PRVA_RAT     2 SMTDLLSAEDIKKAIGAFTAADSFDHKKFFQMVGLKKKSADDVKKVFHILDKDKSGFIEEDELGSILKGFSSDARDLSAKETKTLMAAGDKDGDGKIGVEEFSTLVAES 110
               SCOP domains d1xvja_ A: Parvalbumin                                                                                        SCOP domains
               CATH domains 1xvjA00 A:1-109 EF-hand                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------EF_HAND_2  PDB: A:38-73             ---EF_HAND_2  PDB: A:77-109          PROSITE (1)
                PROSITE (2) --------------------------------------------------EF_HAND_1    --------------------------EF_HAND_1    ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1xvj A   1 SMTDLLSAEDIKKAIGAFTAADSFDHKKFFQMVGLKKKSADDVKKVFHILDKDKSGFIEEDELGSILKGFSSDARDLSAKETKTLMAAGDKDGSGKIEVEEFSTLVAES 109
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with PRVA_RAT | P02625 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:109
                                    11        21        31        41        51        61        71        81        91       101         
             PRVA_RAT     2 SMTDLLSAEDIKKAIGAFTAADSFDHKKFFQMVGLKKKSADDVKKVFHILDKDKSGFIEEDELGSILKGFSSDARDLSAKETKTLMAAGDKDGDGKIGVEEFSTLVAES 110
               SCOP domains d1xvjb_ B: Parvalbumin                                                                                        SCOP domains
               CATH domains 1xvjB00 B:1-109 EF-hand                                                                                       CATH domains
           Pfam domains (1) --EF_hand_5-1xvjB01 B:3-106                                                                               --- Pfam domains (1)
           Pfam domains (2) --EF_hand_5-1xvjB02 B:3-106                                                                               --- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------EF_hand_6-1xvjB03 B:63-108                    - Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------EF_hand_6-1xvjB04 B:63-108                    - Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------EF_HAND_2  PDB: B:38-73             ---EF_HAND_2  PDB: B:77-109          PROSITE (1)
                PROSITE (2) --------------------------------------------------EF_HAND_1    --------------------------EF_HAND_1    ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1xvj B   1 SMTDLLSAEDIKKAIGAFTAADSFDHKKFFQMVGLKKKSADDVKKVFHILDKDKSGFIEEDELGSILKGFSSDARDLSAKETKTLMAAGDKDGSGKIEVEEFSTLVAES 109
                                    10        20        30        40        50        60        70        80        90       100

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, 2)

CATH Domains (1, 2)

Pfam Domains (2, 4)

Gene Ontology (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PRVA_RAT | P02625)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0051480	regulation of cytosolic calcium ion concentration	Any process involved in the maintenance of an internal steady state of calcium ions within the cytosol of a cell or between the cytosol and its surroundings.
cellular component
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0043195	terminal bouton	Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

Visualization

Interactive Views

Asymmetric/Biological Unit
	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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

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

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1xvj
		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
	PRVA_RAT \| P02625
		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