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(-) Description

Title :  CRYSTAL STRUCTURE OF FKBP12
 
Authors :  S. Szep, S. Park, G. D. Vanduyne, J. G. Saven
Date :  30 Apr 07  (Deposition) - 27 May 08  (Release) - 31 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.92
Chains :  Asym./Biol. Unit :  A
Keywords :  High Resolution Protein Structure, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Szep, S. Park, E. T. Boder, G. D. Van Duyne, J. G. Saven
Structural Coupling Between Fkbp12 And Buried Water.
Proteins V. 74 603 2009
PubMed-ID: 18704951  |  Reference-DOI: 10.1002/PROT.22176

(-) Compounds

Molecule 1 - FK506-BINDING PROTEIN 1A
    ChainsA
    EC Number5.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentFKBP12
    GeneFKBP1A, FKBP1, FKBP12
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPEPTIDYL-PROLYL CIS-TRANS ISOMERASE, PPIASE, ROTAMASE, 12 KDA FKBP, FKBP-12, IMMUNOPHILIN FKBP12

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2PPN)

(-) Sites  (0, 0)

(no "Site" information available for 2PPN)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PPN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PPN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PPN)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FKBP_PPIASEPS50059 FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.FKB1A_HUMAN20-108  1A:19-107

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000004001371aENSE00001561754chr20:1373806-1373606201FKB1A_HUMAN1-13131A:1-1212
1.1fENST000004001371fENSE00001107838chr20:1373525-137347848FKB1A_HUMAN13-29171A:12-2817
1.4ENST000004001374ENSE00000858591chr20:1356247-1356135113FKB1A_HUMAN29-66381A:28-6538
1.5aENST000004001375aENSE00000858590chr20:1352884-1352720165FKB1A_HUMAN67-108421A:66-10742
1.7fENST000004001377fENSE00001872186chr20:1350716-13496221095FKB1A_HUMAN-00--

(-) 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:107
 aligned with FKB1A_HUMAN | P62942 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:107
                                    11        21        31        41        51        61        71        81        91       101       
          FKB1A_HUMAN     2 GVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE 108
               SCOP domains d2ppna_ A: FK-506 binding protein (FKBP12), an immunophilin                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------FKBP_C-2ppnA01 A:12-104                                                                      --- Pfam domains
         Sec.struct. author .eeeeeee............eeeeeeeeee....eeeehhhhh..eeee......hhhhhhhhh......eeeeee.hhhh...............eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------FKBP_PPIASE  PDB: A:19-107 UniProt: 20-108                                                PROSITE
           Transcript 1 (1) Exon 1.1a   ---------------Exon 1.4  PDB: A:28-65 UniProt: 29-66 Exon 1.5a  PDB: A:66-107 UniProt: 67-108   Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.1f        ------------------------------------------------------------------------------- Transcript 1 (2)
                 2ppn A   1 GVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE 107
                                    10        20        30        40        50        60        70        80        90       100       

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PPN)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (44, 44)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FKB1A_HUMAN | P62942)
molecular function
    GO:0005528    FK506 binding    Interacting selectively and non-covalently with the 23-membered macrolide lactone FK506.
    GO:0046332    SMAD binding    Interacting selectively and non-covalently with a SMAD signaling protein.
    GO:0048185    activin binding    Interacting selectively and non-covalently with activin, a dimer of inhibin-beta subunits.
    GO:0019855    calcium channel inhibitor activity    Stops, prevents, or reduces the activity of a calcium channel.
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0005527    macrolide binding    Interacting selectively and non-covalently with a macrolide, any of a large group of structurally related antibiotics produced by Streptomyces species.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    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:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0005160    transforming growth factor beta receptor binding    Interacting selectively and non-covalently with the transforming growth factor beta receptor.
    GO:0034713    type I transforming growth factor beta receptor binding    Interacting selectively and non-covalently with a type I transforming growth factor beta receptor.
biological process
    GO:0006458    'de novo' protein folding    The process of assisting in the folding of a nascent peptide chain into its correct tertiary structure.
    GO:0007183    SMAD protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex that contains SMAD proteins.
    GO:0042110    T cell activation    The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:1990000    amyloid fibril formation    The generation of amyloid fibrils, insoluble fibrous protein aggregates exhibiting beta sheet structure, from proteins. An example of this is seen when human RIP1 and RIP3 kinases form a heterodimeric functional amyloid signaling complex (PMID:22817896).
    GO:0070588    calcium ion transmembrane transport    A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0060347    heart trabecula formation    The process of creating a trabecula in the heart. A trabecula is a tissue element in the form of a small beam, strut or rod.
    GO:0051280    negative regulation of release of sequestered calcium ion into cytosol    Any process that stops, prevents, or reduces the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria.
    GO:0060315    negative regulation of ryanodine-sensitive calcium-release channel activity    Any process that decreases the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
    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:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:0031398    positive regulation of protein ubiquitination    Any process that activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0022417    protein maturation by protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that results in the attainment of the full functional capacity of a protein.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
    GO:0042026    protein refolding    The process carried out by a cell that restores the biological activity of an unfolded or misfolded protein, using helper proteins such as chaperones.
    GO:0032925    regulation of activin receptor signaling pathway    Any process that modulates the frequency, rate or extent of the activity of any activin receptor signaling pathway.
    GO:1902991    regulation of amyloid precursor protein catabolic process    Any process that modulates the frequency, rate or extent of amyloid precursor protein catabolic process.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0032880    regulation of protein localization    Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
    GO:0060314    regulation of ryanodine-sensitive calcium-release channel activity    Any process that modulates the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0055010    ventricular cardiac muscle tissue morphogenesis    The process in which the anatomical structures of cardiac ventricle muscle is generated and organized.
cellular component
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0014802    terminal cisterna    The portion of sarcoplasmic reticulum devoted to calcium ion storage and calcium ion release.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FKB1A_HUMAN | P629421a7x 1b6c 1bkf 1bl4 1d6o 1d7h 1d7i 1d7j 1eym 1f40 1fap 1fkb 1fkd 1fkf 1fkg 1fkh 1fki 1fkj 1fkr 1fks 1fkt 1j4h 1j4i 1j4r 1nsg 1qpf 1qpl 1tco 2dg3 2dg4 2dg9 2fap 2fke 2nd5 2ppo 2ppp 2rse 3fap 3h9r 3mdy 4dh0 4fap 4ipx 4n19 4odp 4odq 4odr 5i7p 5i7q

(-) Related Entries Specified in the PDB File

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