Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF S100B IN THE CALCIUM AND ZINC LOADED STATE AT PH 10.0
 
Authors :  T. Ostendorp, J. Diez, C. W. Heizmann, G. Fritz
Date :  02 May 08  (Deposition) - 14 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  S100B, S100, Ef-Hand, Metal-Binding, Nucleus, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Ostendorp, J. Diez, C. W. Heizmann, G. Fritz
The Crystal Structures Of Human S100B In The Zinc- And Calcium-Loaded State At Three Ph Values Reveal Zinc Ligand Swapping.
Biochim. Biophys. Acta V. 1813 1083 2011
PubMed-ID: 20950652  |  Reference-DOI: 10.1016/J.BBAMCR.2010.10.006

(-) Compounds

Molecule 1 - PROTEIN S100-B
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEMEX-2
    Expression System StrainBL21(DE3)
    Expression System Vector TypePLASMID
    GeneS100B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymS100 CALCIUM-BINDING PROTEIN B, S-100 PROTEIN SUBUNIT BETA, S-100 PROTEIN BETA CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2PGE1Ligand/IonTRIETHYLENE GLYCOL
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:61 , ASP A:63 , ASP A:65 , GLU A:67 , GLU A:72BINDING SITE FOR RESIDUE CA A 92
2AC2SOFTWARESER A:18 , GLU A:21 , ASP A:23 , LYS A:26 , GLU A:31BINDING SITE FOR RESIDUE CA A 93
3AC3SOFTWARESER B:18 , GLU B:21 , ASP B:23 , LYS B:26 , GLU B:31BINDING SITE FOR RESIDUE CA B 92
4AC4SOFTWAREASP B:61 , ASP B:63 , ASP B:65 , GLU B:67 , GLU B:72BINDING SITE FOR RESIDUE CA B 93
5AC5SOFTWAREHIS A:15 , HIS A:25 , HIS B:85 , GLU B:89BINDING SITE FOR RESIDUE ZN A 94
6AC6SOFTWAREHIS A:85 , GLU A:89 , HIS B:15 , HIS B:25BINDING SITE FOR RESIDUE ZN A 95

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D10)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:89 -His A:90

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D10)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S100B_HUMAN49-84
 
  2A:48-83
B:48-83
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S100B_HUMAN57-78
 
  2A:56-77
B:56-77
3EF_HAND_1PS00018 EF-hand calcium-binding domain.S100B_HUMAN62-74
 
  2A:61-73
B:61-73

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003976482aENSE00001529559chr21:48022806-48022191616S100B_HUMAN1-46462A:0-45
B:0-45
46
46
1.4aENST000003976484aENSE00001529558chr21:48019416-48019194223S100B_HUMAN47-92462A:46-91
B:46-90
46
45

(-) 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:92
 aligned with S100B_HUMAN | P04271 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:92
                                    10        20        30        40        50        60        70        80        90  
           S100B_HUMAN    1 MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDNDGDGECDFQEFMAFVAMVTTACHEFFEHE 92
               SCOP domains d3d10a_ A: Calcyclin (S100)                                                                  SCOP domains
               CATH domains 3d10A00 A:0-91 EF-hand                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........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 1.2a  PDB: A:0-45 UniProt: 1-46          Exon 1.4a  PDB: A:46-91 UniProt: 47-92         Transcript 1
                  3d10 A  0 MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDNDGDGECDFQEFMAFVAMVTTACHEFFEHE 91
                                     9        19        29        39        49        59        69        79        89  

Chain B from PDB  Type:PROTEIN  Length:91
 aligned with S100B_HUMAN | P04271 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:91
                                    10        20        30        40        50        60        70        80        90 
           S100B_HUMAN    1 MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDNDGDGECDFQEFMAFVAMVTTACHEFFEH 91
               SCOP domains d3d10b_ B: Calcyclin (S100)                                                                 SCOP domains
               CATH domains 3d10B00 B:0-90 EF-hand                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........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 1.2a  PDB: B:0-45 UniProt: 1-46          Exon 1.4a  PDB: B:46-90 UniProt: 47-92        Transcript 1
                  3d10 B  0 MSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDNDGDGECDFQEFMAFVAMVTTACHEFFEH 90
                                     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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D10)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (S100B_HUMAN | P04271)
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: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:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    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:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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.

 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 ]
    PGE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:89 - His A:90   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3d10
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  S100B_HUMAN | P04271
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  S100B_HUMAN | P04271
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        S100B_HUMAN | P042711mq1 1uwo 2h61 2m49 2pru 3czt 3d0y 3hcm 4xyn 5csf 5csi 5csj 5csn 5d7f

(-) Related Entries Specified in the PDB File

1xyd NMR SOLUTION STRUCTURE OF RAT ZINC-CALCIUM-S100B
2h61 X-RAY STRUCTURE OF HUMAN CA2+-LOADED S100B
3czt CRYSTAL STRUCTURE OF S100B IN THE CALCIUM AND ZINC LOADED STATE AT PH 9.0
3doy CRYSTAL STRUCTURE OF S100B IN THE CALCIUM AND ZINC LOADED STATE AT PH 6.5