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(-) Description

Title :  HUMAN PSORIASIN (S100A7) CA2+ BOUND FORM (CRYSTAL FORM I)
 
Authors :  D. E. Brodersen, J. Nyborg, M. Kjeldgaard
Date :  17 Sep 98  (Deposition) - 15 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ca-Binding, Psoriasis, S100 Protein Family, X-Ray Crystallography, Ef-Hand Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. E. Brodersen, J. Nyborg, M. Kjeldgaard
Zinc-Binding Site Of An S100 Protein Revealed. Two Crystal Structures Of Ca2+-Bound Human Psoriasin (S100A7) In The Zn2+-Loaded And Zn2+-Free States.
Biochemistry V. 38 1695 1999
PubMed-ID: 10026247  |  Reference-DOI: 10.1021/BI982483D
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PSORIASIN
    CellKERATINOCYTES
    Cellular LocationCYTOPLASMIC, OR MAY BE SECRETED BY A NON-CLASSICAL SECRETORY PATHWAY
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPT7H6FX-PS.4
    Expression System StrainBL21
    Expression System Taxid511693
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCHAIN A IS CA2+ AND ZN2+ BOUND FORM, CHAIN B IS CA2+ BOUND FORM
    SynonymS100A7

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2ZN1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:62 , ASN A:64 , ASP A:66 , LYS A:68 , GLU A:73 , HOH A:269BINDING SITE FOR RESIDUE CA A 102
2AC2SOFTWAREHIS A:17 , ASP A:24 , HIS B:86 , HIS B:90BINDING SITE FOR RESIDUE ZN A 103
3AC3SOFTWAREASP B:62 , ASN B:64 , ASP B:66 , LYS B:68 , GLU B:73 , HOH B:270BINDING SITE FOR RESIDUE CA B 102
4CAAUNKNOWNASP A:62 , ASN A:64 , ASP A:66 , LYS A:68 , GLU A:73REGULATORY CA2+ BINDING SITE
5CABUNKNOWNASP B:62 , ASN B:64 , ASP B:66 , LYS A:68 , GLU B:73REGULATORY CA2+ BINDING SITE
6ZNAUNKNOWNHIS A:17 , ASP A:24 , HIS B:86 , HIS B:90ZN2+ BINDING SITE

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:46 -A:95
2B:46 -B:95

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_039118E28DS10A7_HUMANPolymorphism3014837A/BD27D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S10A7_HUMAN50-85
 
  2A:49-84
B:49-84
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S10A7_HUMAN58-79
 
  2A:57-78
B:57-78
3EF_HAND_1PS00018 EF-hand calcium-binding domain.S10A7_HUMAN63-75
 
  2A:62-74
B:62-74

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003687231ENSE00001447846chr1:153433177-15343308494S10A7_HUMAN-00--
1.3ENST000003687233ENSE00001604429chr1:153431506-153431349158S10A7_HUMAN1-47472A:1-46
B:1-46
46
46
1.4ENST000003687234ENSE00001447844chr1:153430446-153430220227S10A7_HUMAN48-101542A:47-96
B:47-96
50
50

(-) 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:96
 aligned with S10A7_HUMAN | P31151 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:96
                                    11        21        31        41        51        61        71        81        91      
           S10A7_HUMAN    2 SNTQAERSIIGMIDMFHKYTRRDDKIEKPSLLTMMKENFPNFLSACDKKGTNYLADVFEKKDKNEDKKIDFSEFLSLLGDIATDYHKQSHGAAPCS 97
               SCOP domains d3psra_ A: Calcyclin (S100)                                                                      SCOP domains
               CATH domains 3psrA00 A:1-96 EF-hand                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhh....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------D--------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: A:49-84             ------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: A:57-7------------------ PROSITE (2)
                PROSITE (3) -------------------------------------------------------------EF_HAND_1    ---------------------- PROSITE (3)
               Transcript 1 Exon 1.3  PDB: A:1-46 UniProt: 1-47           Exon 1.4  PDB: A:47-96 UniProt: 48-101             Transcript 1
                  3psr A  1 SNTQAERSIIGMIDMFHKYTRRDDKIDKPSLLTMMKENFPNFLSACDKKGTNYLADVFEKKDKNEDKKIDFSEFLSLLGDIATDYHKQSHGAAPCS 96
                                    10        20        30        40        50        60        70        80        90      

Chain B from PDB  Type:PROTEIN  Length:96
 aligned with S10A7_HUMAN | P31151 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:96
                                    11        21        31        41        51        61        71        81        91      
           S10A7_HUMAN    2 SNTQAERSIIGMIDMFHKYTRRDDKIEKPSLLTMMKENFPNFLSACDKKGTNYLADVFEKKDKNEDKKIDFSEFLSLLGDIATDYHKQSHGAAPCS 97
               SCOP domains d3psrb_ B: Calcyclin (S100)                                                                      SCOP domains
               CATH domains 3psrB00 B:1-96 EF-hand                                                                           CATH domains
           Pfam domains (1) ----S_100-3psrB01 B:5-45                     --------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----S_100-3psrB02 B:5-45                     --------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhh....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------D--------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: B:49-84             ------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: B:57-7------------------ PROSITE (2)
                PROSITE (3) -------------------------------------------------------------EF_HAND_1    ---------------------- PROSITE (3)
               Transcript 1 Exon 1.3  PDB: B:1-46 UniProt: 1-47           Exon 1.4  PDB: B:47-96 UniProt: 48-101             Transcript 1
                  3psr B  1 SNTQAERSIIGMIDMFHKYTRRDDKIDKPSLLTMMKENFPNFLSACDKKGTNYLADVFEKKDKNEDKKIDFSEFLSLLGDIATDYHKQSHGAAPCS 96
                                    10        20        30        40        50        60        70        80        90      

   Legend:   → Mismatch (orange background)
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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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (S10A7_HUMAN | P31151)
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: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:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0008544    epidermis development    The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0030216    keratinocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0010820    positive regulation of T cell chemotaxis    Any process that increases the rate, frequency or extent of T cell chemotaxis. T cell chemotaxis is the directed movement of a T cell in response to an external stimulus.
    GO:0071624    positive regulation of granulocyte chemotaxis    Any process that increases the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus.
    GO:0090026    positive regulation of monocyte chemotaxis    Any process that increases the frequency, rate, or extent of monocyte chemotaxis.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0000302    response to reactive oxygen species    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 reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
    GO:0051238    sequestering of metal ion    The process of binding or confining metal ions such that they are separated from other components of a biological system.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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: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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        S10A7_HUMAN | P311511psr 2psr 2wnd 2wor 2wos 4aqj

(-) Related Entries Specified in the PDB File

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