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(-) Description

Title :  X-RAY STRUCTURE OF BOVINE SC0322,CA(2+)-S100B
 
Authors :  T. H. Charpentier, D. J. Weber, P. W. Wilder
Date :  26 Jan 10  (Deposition) - 29 Dec 10  (Release) - 29 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ef Hand, Alpha Helical, Metal-Binding, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. T. Wilder, T. H. Charpentier, M. A. Liriano, K. Gianni, K. M. Varney, E. Pozharski, A. Coop, E. A. Toth, A. D. Mackerell, D. J. Weber
In Vitro Screening And Structural Characterization Of Inhibitors Of The S100B-P53 Interaction.
Int J High Throughput Screen V. 2010 109 2010
PubMed-ID: 21132089  |  Reference-DOI: 10.2147/IJHTS.S8210

(-) Compounds

Molecule 1 - PROTEIN S100-B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneS100B
    Organism CommonBOVINE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymS100 CALCIUM-BINDING PROTEIN B, S-100 PROTEIN SUBUNIT BETA, S-100 PROTEIN BETA CHAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EMC1Ligand/IonETHYL MERCURY ION
3JKE1Ligand/Ion2-SULFANYLBENZOIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EMC2Ligand/IonETHYL MERCURY ION
3JKE2Ligand/Ion2-SULFANYLBENZOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:61 , ASP A:63 , ASP A:65 , GLU A:67 , GLU A:72 , HOH A:105BINDING SITE FOR RESIDUE CA A 90
2AC2SOFTWARESER A:18 , GLU A:21 , ASP A:23 , LYS A:26 , GLU A:31 , HOH A:120BINDING SITE FOR RESIDUE CA A 91
3AC3SOFTWARECYS A:84 , PHE A:87 , HOH A:126BINDING SITE FOR RESIDUE EMC A 92
4AC4SOFTWARETHR A:59BINDING SITE FOR RESIDUE JKE A 93

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LK1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LK1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LK1)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S100B_BOVIN49-84  1A:48-83
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S100B_BOVIN57-78  1A:56-77
3EF_HAND_1PS00018 EF-hand calcium-binding domain.S100B_BOVIN62-74  1A:61-73
Biological Unit 1 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S100B_BOVIN49-84  2A:48-83
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S100B_BOVIN57-78  2A:56-77
3EF_HAND_1PS00018 EF-hand calcium-binding domain.S100B_BOVIN62-74  2A:61-73

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000062751ENSBTAE00000256656chr1:149249251-14924919953S100B_BOVIN-00--
1.2ENSBTAT000000062752ENSBTAE00000256655chr1:149246090-149245953138S100B_BOVIN1-46461A:0-4546
1.3ENSBTAT000000062753ENSBTAE00000050031chr1:149243137-1492418491289S100B_BOVIN47-92461A:46-8742

(-) Sequences/Alignments

Asymmetric 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:88
 aligned with S100B_BOVIN | P02638 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:88
                                    10        20        30        40        50        60        70        80        
           S100B_BOVIN    1 MSELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEF 88
               SCOP domains d3lk1a_ A: Calcyclin (S100)                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---S_100-3lk1A01 A:3-46                        -----efhand-3lk1A02 A:52-80       ------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhh........hhhhhhhhhhhhh......eehhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: A:48-83             ---- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: A:56-7---------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------EF_HAND_1    -------------- PROSITE (3)
               Transcript 1 Exon 1.2  PDB: A:0-45 UniProt: 1-46           Exon 1.3  PDB: A:46-87 UniProt: 47-92      Transcript 1
                  3lk1 A  0 MSELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEF 87
                                     9        19        29        39        49        59        69        79        

   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)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LK1)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A   (S100B_BOVIN | P02638)
molecular function
    GO:0050786    RAGE receptor binding    Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products.
    GO:0044548    S100 protein binding    Interacting selectively and non-covalently with a S100 protein. S100 is a small calcium and zinc binding protein produced in astrocytes that is implicated in Alzheimer's disease, Down Syndrome and ALS.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0048306    calcium-dependent 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), in the presence of calcium.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0019210    kinase inhibitor activity    Stops, prevents or reduces the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0048156    tau protein binding    Interacting selectively and non-covalently with tau protein. tau is a microtubule-associated protein, implicated in Alzheimer's disease, Down Syndrome and ALS.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0048143    astrocyte activation    A change in morphology and behavior of an astrocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0007611    learning or memory    The acquisition and processing of information and/or the storage and retrieval of this information over time.
    GO:0007613    memory    The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
    GO:0071638    negative regulation of monocyte chemotactic protein-1 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of production of monocyte chemotactic protein-1.
    GO:0042326    negative regulation of phosphorylation    Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0045917    positive regulation of complement activation    Any process that activates or increases the frequency, rate or extent of complement activation.
    GO:0048168    regulation of neuronal synaptic plasticity    A process that modulates neuronal synaptic plasticity, the ability of neuronal synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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 Related Entries

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

UniProtKB/Swiss-Prot
        S100B_BOVIN | P026381cfp 1mho 1psb 3cr2 3cr4 3cr5 3gk1 3gk2 3gk4 3iqo 3iqq 3lk0 3lle 3rlz 3rm1 4fqo 4pdz 4pe0 4pe1 4pe4 4pe7 5dkn 5dkq 5dkr 5er4 5er5

(-) Related Entries Specified in the PDB File

3lk0 X-RAY STRUCTURE OF BOVINE SC0067,CA(2+)-S100B