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(-) Description

Title :  STRUCTURE OF THE R75A MUTANT OF RAT ALPHA-PARVALBUMIN
 
Authors :  F. Hoh, A. Padilla
Date :  31 Oct 08  (Deposition) - 07 Jul 09  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Calcium Binding Protein, Ef-Hand, Acetylation, Calcium, Muscle Protein, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Hoh, A. Cave, M. P. Strub, J. L. Baneres, A. Padilla
Removing The Invariant Salt Bridge Of Parvalbumin Increases Flexibility In The Ab-Loop Structure
Acta Crystallogr. , Sect. D V. 65 733 2009
PubMed-ID: 19622856  |  Reference-DOI: 10.1107/S0907444909011482
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PARVALBUMIN ALPHA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEMEX
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PVALB, PVA
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:51 , ASP A:53 , SER A:55 , PHE A:57 , GLU A:59 , GLU A:62BINDING SITE FOR RESIDUE CA A 110
2AC2SOFTWAREASP A:90 , ASP A:92 , ASP A:94 , LYS A:96 , GLU A:101 , HOH A:158BINDING SITE FOR RESIDUE CA A 111
3AC3SOFTWARESER A:78 , ALA A:79 , GLY A:98 , VAL A:99 , GLU A:100 , HOH A:125 , HOH A:134 , HOH A:193 , HOH A:247BINDING SITE FOR RESIDUE SO4 A 112
4AC4SOFTWAREHIS A:48 , LYS A:68 , ALA A:75 , ASP A:76 , HOH A:226BINDING SITE FOR RESIDUE SO4 A 113

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F45)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F45)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F45)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.PRVA_RAT39-74
78-110		  2A:38-73
A:77-109
2EF_HAND_1PS00018 EF-hand calcium-binding domain.PRVA_RAT52-64
91-103		  2A:51-63
A:90-102

(-) Exons   (0, 0)

(no "Exon" information available for 3F45)

(-) 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 d3f45a_ A: Parvalbumin                                                                                        SCOP domains
               CATH domains 3f45A00 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
                 3f45 A   1 SMTDLLSAEDIKKAIGAFTAADSFDHKKFFQMVGLKKKSADDVKKVFHILDKDKSGFIEEDELGSILKGFSSDAADLSAKETKTLMAAGDKDGDGKIGVEEFSTLVAES 109
                                    10        20        30        40        50        60        70        80        90       100
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  - → Gap (green background, '-', border residues have a numbering label)
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  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)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F45)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

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  3f45
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  PRVA_RAT | P02625
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PRVA_RAT | P02625: 1g33 1rtp 1rwy 1s3p 1xvj 2jww

(-) Related Entries Specified in the PDB File

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