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(-) Description

Title :  THREE-DIMENSIONAL SOLUTION STRUCTURE OF APO-S100P PROTEIN DETERMINED BY NMR SPECTROSCOPY
 
Authors :  Y. -C. Lee, D. E. Volk, V. Thiviyanathan, Q. Kleerekoper, A. V. Gribenko, S. Zhang, D. G. Gorenstein, G. I. Makhatadze, B. A. Luxo
Date :  09 Apr 03  (Deposition) - 20 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (16x)
Keywords :  Ef-Hand, S100 Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. -C. Lee, D. E. Volk, V. Thiviyanathan, Q. Kleerekoper, A. V. Gribenko, S. Zhang, D. G. Gorenstein, G. I. Makhatadze, B. A. Luxon
Nmr Structure Of The Apo-S100P Protein.
J. Biomol. Nmr V. 29 399 2004
PubMed-ID: 15213440  |  Reference-DOI: 10.1023/B:JNMR.0000032617.88899.4B
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - S-100P PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: S100P OR S100E
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  
NMR Structure (16x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1OZO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 7)

NMR Structure
No.ModelResidues
17, 8, 9, 10, 14Gln B:26 -Thr B:27
29, 10Gln A:26 -Thr A:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.S100P_HUMAN49-84
 		  2A:49-84
B:49-84
2S100_CABPPS00303 S-100/ICaBP type calcium binding protein signature.S100P_HUMAN57-78
 		  2A:57-78
B:57-78

(-) Exons   (2, 4)

NMR Structure (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002963701aENSE00001080327chr4:6694796-66957971002S100P_HUMAN1-46462A:1-46
B:1-46		46
46
1.2aENST000002963702aENSE00001080326chr4:6698620-6698896277S100P_HUMAN47-95492A:47-95
B:47-95		49
49

(-) 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:95
 aligned with S100P_HUMAN | P25815 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:95
                                    10        20        30        40        50        60        70        80        90     
           S100P_HUMAN    1 MTELETAMGMIIDVFSRYSGSEGSTQTLTKGELKVLMEKELPGFLQSGKDKDAVDKLLKDLDANGDAQVDFSEFIVFVAAITSACHKYFEKAGLK 95
               SCOP domains d1ozoa_ A: Calcyclin (S100)                                                                     SCOP domains
               CATH domains 1ozoA00 A:1-95 EF-hand                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.......eeehhhhhhhhhhhh.hhhhh.......hhhhhhhhh....eeehhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: A:49-84             ----------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: A:57-7----------------- PROSITE (2)
               Transcript 1 Exon 1.1a  PDB: A:1-46 UniProt: 1-46          Exon 1.2a  PDB: A:47-95 UniProt: 47-95            Transcript 1
                  1ozo A  1 MTELEAAMGMIIDVFSRYSGSEGSTQTLTKGELKVLMEKELPGFLQSGKDKDAVDKLLKDLDANGDAQVDFSEFIVFVAAITSASHKYFEKTGLK 95
                                    10        20        30        40        50        60        70        80        90     


Chain B from PDB  Type:PROTEIN  Length:95
 aligned with S100P_HUMAN | P25815 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:95
                                    10        20        30        40        50        60        70        80        90     
           S100P_HUMAN    1 MTELETAMGMIIDVFSRYSGSEGSTQTLTKGELKVLMEKELPGFLQSGKDKDAVDKLLKDLDANGDAQVDFSEFIVFVAAITSACHKYFEKAGLK 95
               SCOP domains d1ozob_ B: Calcyclin (S100)                                                                     SCOP domains
               CATH domains 1ozoB00 B:1-95 EF-hand                                                                          CATH domains
           Pfam domains (1) ---S_100-1ozoB01 B:4-47                        ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---S_100-1ozoB02 B:4-47                        ------------------------------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh.........eehhhhh.hhhhhh.hhhhh.......hhhhhhhhhhh..eehhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------EF_HAND_2  PDB: B:49-84             ----------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------S100_CABP  PDB: B:57-7----------------- PROSITE (2)
               Transcript 1 Exon 1.1a  PDB: B:1-46 UniProt: 1-46          Exon 1.2a  PDB: B:47-95 UniProt: 47-95            Transcript 1
                  1ozo B  1 MTELEAAMGMIIDVFSRYSGSEGSTQTLTKGELKVLMEKELPGFLQSGKDKDAVDKLLKDLDANGDAQVDFSEFIVFVAAITSASHKYFEKTGLK 95
                                    10        20        30        40        50        60        70        80        90
   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  (1, 2)

NMR Structure
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A,B   (S100P_HUMAN | P25815)
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: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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) 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).
biological process
    GO:0043542    endothelial cell migration    The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0010033    response to organic substance    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 an organic substance stimulus.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031528    microvillus membrane    The portion of the plasma membrane surrounding a microvillus.
    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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    Gln A:26 - Thr A:27   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        S100P_HUMAN | P25815: 1j55 2mjw

(-) Related Entries Specified in the PDB File

1j55 THE CRYSTAL STRUCTURE OF CA+-BOUND HUMAN S100P