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(-) Description

Title :  THE THREE-DIMENSIONAL STRUCTURE OF HUMAN S100A12
 
Authors :  O. V. Moroz, A. A. Antson, G. N. Murshudov, N. J. Maitland, G. G. Dodson, K. S. Wilson, I. Skibshoj, E. M. Lukanidin, I. B. Bronstein
Date :  18 Sep 00  (Deposition) - 08 Jan 01  (Release) - 16 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antifungal Protein, S100 Protein, X-Ray Structure, Ef-Hand, Calcium Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. V. Moroz, A. A. Antson, G. N. Murshudov, N. J. Maitland, G. G. Dodson, K. S. Wilson, I. Skibshoj, E. M. Lukanidin, I. B. Bronstein
The Three-Dimensional Structure Of Human S100A12
Acta Crystallogr. , Sect. D V. 57 20 2001
PubMed-ID: 11134923  |  Reference-DOI: 10.1107/S090744490001458X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - S100A12
    Cell: GRANULOCYTE
    Chains: A, B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CALGRANULIN C
    Tissue: BLOOD

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:18 , LYS A:21 , HIS A:23 , THR A:26 , GLU A:31 , HOH A:2087BINDING SITE FOR RESIDUE CA A1089
2AC2SOFTWAREASP A:61 , ASN A:63 , ASP A:65 , GLN A:67 , GLU A:72 , HOH A:2084BINDING SITE FOR RESIDUE CA A1090
3AC3SOFTWARESER B:18 , LYS B:21 , HIS B:23 , THR B:26 , GLU B:31 , HOH B:2064BINDING SITE FOR RESIDUE CA B1089
4AC4SOFTWAREASP B:61 , ASN B:63 , ASP B:65 , GLN B:67 , GLU B:72 , HOH B:2061BINDING SITE FOR RESIDUE CA B1090

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E8A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E8A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E8A)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S10AC_HUMAN49-84
 		  2A:48-83
B:48-83
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S10AC_HUMAN57-78
 		  2A:56-77
B:56-77

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003687371aENSE00001935189chr1:153348125-15334802898S10AC_HUMAN-00--
1.2ENST000003687372ENSE00001072568chr1:153347088-153346931158S10AC_HUMAN1-46462A:1-45
B:1-45		45
45
1.4aENST000003687374aENSE00001447874chr1:153346443-153346184260S10AC_HUMAN47-92462A:46-87
B:46-88		42
43

(-) 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:87
 aligned with S10AC_HUMAN | P80511 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:87
                                    11        21        31        41        51        61        71        81       
           S10AC_HUMAN    2 TKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGLDANQDEQVDFQEFISLVAIALKAAHYH 88
               SCOP domains d1e8aa_ A: Calcyclin (S100)                                                             SCOP domains
               CATH domains 1e8aA00 A:1-87 EF-hand                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh 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)
               Transcript 1 Exon 1.2  PDB: A:1-45 UniProt: 1-46          Exon 1.4a  PDB: A:46-87 UniProt: 47-92     Transcript 1
                  1e8a A  1 TKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGLDANQDEQVDFQEFISLVAIALKAAHYH 87
                                    10        20        30        40        50        60        70        80       


Chain B from PDB  Type:PROTEIN  Length:88
 aligned with S10AC_HUMAN | P80511 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:88
                                    11        21        31        41        51        61        71        81        
           S10AC_HUMAN    2 TKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGLDANQDEQVDFQEFISLVAIALKAAHYHT 89
               SCOP domains d1e8ab_ B: Calcyclin (S100)                                                              SCOP domains
               CATH domains 1e8aB00 B:1-88 EF-hand                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.. 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)
               Transcript 1 Exon 1.2  PDB: B:1-45 UniProt: 1-46          Exon 1.4a  PDB: B:46-88 UniProt: 47-92      Transcript 1
                  1e8a B  1 TKLEEHLEGIVNIFHQYSVRKGHFDTLSKGELKQLLTKELANTIKNIKDKAVIDEIFQGLDANQDEQVDFQEFISLVAIALKAAHYHT 88
                                    10        20        30        40        50        60        70        80
   Legend:   → Mismatch (orange background)
  - → 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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E8A)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (S10AC_HUMAN | P80511)
molecular function
    GO:0050786    RAGE receptor binding    Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0050663    cytokine secretion    The regulated release of cytokines from a cell. Cytokines are any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
    GO:0045576    mast cell activation    The change in morphology and behavior of a mast cell resulting from exposure to a cytokine, chemokine, soluble factor, or to (at least in mammals) an antigen which the mast cell has specifically bound via IgE bound to Fc-epsilonRI receptors.
    GO:0002548    monocyte chemotaxis    The movement of a monocyte in response to an external stimulus.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    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:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0006805    xenobiotic metabolic process    The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        S10AC_HUMAN | P80511: 1gqm 1odb 2m9g 2wc8 2wcb 2wce 2wcf

(-) Related Entries Specified in the PDB File

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