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(-) Description

Title :  SOLUTION STRUCTURE OF RAT APO-S100B USING DIPOLAR COUPLINGS
 
Authors :  D. J. Weber, A. C. Drohat, N. Tjandra, D. M. Baldisseri
Date :  17 Dec 98  (Deposition) - 30 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (21x)
Keywords :  S100Beta, S100B, Nmr, Dipolar Couplings, Ef-Hand, S100 Protein, Calcium- Binding Protein, Four-Helix Bundle, Three- Dimensional Structure, Solution Structure, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Drohat, N. Tjandra, D. M. Baldisseri, D. J. Weber
The Use Of Dipolar Couplings For Determining The Solution Structure Of Rat Apo-S100B(Betabeta).
Protein Sci. V. 8 800 1999
PubMed-ID: 10211826
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (S-100 PROTEIN, BETA CHAIN)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11B
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 562
    Gene: S100BETA FROM RATTUS NORVEGICUS (RAT)
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: S100B IS A HOMODIMER OF S100BETA SUBUNITS
    Other Details - Source: SEE MAIN REFERENCE
    Synonym: S100B, S100BETA

 Structural Features

(-) Chains, Units

  
NMR Structure (21x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1B4C)

(-) Sites  (0, 0)

(no "Site" information available for 1B4C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B4C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B4C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B4C)

(-) PROSITE Motifs  (3, 6)

NMR Structure (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S100B_RAT49-84
 		  2A:48-83
B:48-83
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S100B_RAT57-78
 		  2A:56-77
B:56-77
3EF_HAND_1PS00018 EF-hand calcium-binding domain.S100B_RAT62-74
 		  2A:61-73
B:61-73

(-) Exons   (2, 4)

NMR Structure (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000017431ENSRNOE00000012113chr20:12824508-12824397112S100B_RAT-00--
1.2ENSRNOT000000017432ENSRNOE00000012114chr20:12796288-12796143146S100B_RAT1-46462A:0-45
B:0-45		46
46
1.3ENSRNOT000000017433ENSRNOE00000012115chr20:12792665-127914401226S100B_RAT47-92462A:46-91
B:46-91		46
46

(-) 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:92
 aligned with S100B_RAT | P04631 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:92
                                    10        20        30        40        50        60        70        80        90  
             S100B_RAT    1 MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDEDGDGECDFQEFMAFVSMVTTACHEFFEHE 92
               SCOP domains d1b4ca_ A: Calcyclin (S100)                                                                  SCOP domains
               CATH domains 1b4cA00 A:0-91 EF-hand                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh.hhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.. 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:46-91 UniProt: 47-92          Transcript 1
                  1b4c A  0 MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDEDGDGECDFQEFMAFVSMVTTACHEFFEHE 91
                                     9        19        29        39        49        59        69        79        89  


Chain B from PDB  Type:PROTEIN  Length:92
 aligned with S100B_RAT | P04631 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:92
                                    10        20        30        40        50        60        70        80        90  
             S100B_RAT    1 MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDEDGDGECDFQEFMAFVSMVTTACHEFFEHE 92
               SCOP domains d1b4cb_ B: Calcyclin (S100)                                                                  SCOP domains
               CATH domains 1b4cB00 B:0-91 EF-hand                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh.hhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: B:48-83             -------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: B:56-7-------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------EF_HAND_1    ------------------ PROSITE (3)
               Transcript 1 Exon 1.2  PDB: B:0-45 UniProt: 1-46           Exon 1.3  PDB: B:46-91 UniProt: 47-92          Transcript 1
                  1b4c B  0 MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDEDGDGECDFQEFMAFVSMVTTACHEFFEHE 91
                                     9        19        29        39        49        59        69        79        89
   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)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B4C)

(-) Gene Ontology  (32, 32)

NMR Structure(hide GO term definitions)
Chain A,B   (S100B_RAT | P04631)
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: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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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:0048708    astrocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an astrocyte. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function.
    GO:0071456    cellular response to hypoxia    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0007611    learning or memory    The acquisition and processing of information and/or the storage and retrieval of this information over time.
    GO:0060291    long-term synaptic potentiation    A process that modulates synaptic plasticity such that synapses are changed resulting in the increase in the rate, or frequency of synaptic transmission at the synapse.
    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:2001015    negative regulation of skeletal muscle cell differentiation    Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle cell differentiation.
    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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0050806    positive regulation of synaptic transmission    Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    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:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0051597    response to methylmercury    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methylmercury stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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

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UniProtKB/Swiss-Prot
        S100B_RAT | P04631: 1dt7 1mwn 1qlk 1sym 1xyd 2k7o

(-) Related Entries Specified in the PDB File

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