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(-) Description

Title :  CRYSTAL STRUCTURE OF A MULTI-DOMAIN IMMUNOPHILIN FROM ARABIDOPSIS THALIANA
 
Authors :  J. Granzin, A. Eckhoff, O. H. Weiergraeber
Date :  20 Sep 06  (Deposition) - 31 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Fkbp-Like, Alpha-Beta, Tpr-Like, Alpha, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Granzin, A. Eckhoff, O. H. Weiergraber
Crystal Structure Of A Multi-Domain Immunophilin From Arabidopsis Thaliana: A Paradigm For Regulation Of Plant Abc Transporters.
J. Mol. Biol. V. 364 799 2006
PubMed-ID: 17045295  |  Reference-DOI: 10.1016/J.JMB.2006.09.052
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATFKBP42
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET28A
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentFKBP-TYPE DOMAIN AND TPR DOMAIN, RESIDUES 1-339
    GeneFKBP42, TWD1, UCU2
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    StrainECOTYPE COLUMBIA
    SynonymTWD1 (TWISTED DWARF 1)

 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 2IF4)

(-) Sites  (0, 0)

(no "Site" information available for 2IF4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IF4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IF4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IF4)

(-) PROSITE Motifs  (3, 4)

Asymmetric/Biological Unit (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FKBP_PPIASEPS50059 FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.FKB42_ARATH67-159  1A:67-159
2TPRPS50005 TPR repeat profile.FKB42_ARATH179-212
264-297
  2A:179-212
A:264-292
3TPR_REGIONPS50293 TPR repeat region circular profile.FKB42_ARATH179-212
230-297
  2A:179-212
A:230-292

(-) Exons   (0, 0)

(no "Exon" information available for 2IF4)

(-) 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:258
 aligned with FKB42_ARATH | Q9LDC0 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:258
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284        
          FKB42_ARATH    35 NVPPKVDSEAEVLDEKVSKQIIKEGHGSKPSKYSTCFLHYRAWTKNSQHKFEDTWHEQQPIELVLGKEKKELAGLAIGVASMKSGERALVHVGWELAYGKEGNFSFPNVPPMADLLYEVEVIGFDETKEGKARSDMTVEERIGAADRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQK 292
               SCOP domains d2if4a1 A:35-160 automated matches                                                                                            d2if4a2 A:161-292 automated matches                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeee..eeeeeee...........eeeeeeeeee.......eehhhhh..eeee....hhhhhhhhhhhhhh....eeeeee.hhhh.................eeeeeeeeeee...........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------FKBP_PPIASE  PDB: A:67-159 UniProt: 67-159                                                   -------------------TPR  PDB: A:179-212               ---------------------------------------------------TPR  PDB: A:264-292           PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------TPR_REGION  PDB: A:179-212        -----------------TPR_REGION  PDB: A:230-292 UniProt: 230-297                     PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2if4 A  35 NVPPKVDSEAEVLDEKVSKQIIKEGHGSKPSKYSTCFLHYRAWTKNSQHKFEDTWHEQQPIELVLGKEKKELAGLAIGVASMKSGERALVHVGWELAYGKEGNFSFPNVPPMADLLYEVEVIGFDETKEGKARSDMTVEERIGAADRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQK 292
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284        

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IF4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IF4)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FKB42_ARATH | Q9LDC0)
molecular function
    GO:0005528    FK506 binding    Interacting selectively and non-covalently with the 23-membered macrolide lactone FK506.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    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: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).
biological process
    GO:0009734    auxin-activated signaling pathway    A series of molecular signals generated by the binding of the plant hormone auxin to a receptor, and ending with modulation of a downstream cellular process, e.g. transcription.
    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:0048366    leaf development    The process whose specific outcome is the progression of the leaf over time, from its formation to the mature structure.
    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:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
cellular component
    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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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 Related Entries

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        FKB42_ARATH | Q9LDC02f4e

(-) Related Entries Specified in the PDB File

2f4e N-TERMINAL DOMAIN OF FKBP42 FROM ARABIDOPSIS THALIANA