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(-) Description

Title :  SOLUTION STRUCTURE OF FOURTH PDZ DOMAIN OF PDZ DOMAIN CONTAINING PROTEIN 1
 
Authors :  T. N. Niraula, T. Tomizawa, K. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  15 Feb 07  (Deposition) - 26 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdz Domain, Regulatory Factor, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. N. Niraula, T. Tomizawa, K. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of Fourth Pdz Domain Of Pdz Domain Containing Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PDZ DOMAIN-CONTAINING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression System PlasmidP050905-18
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GenePDZK1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymCFTR-ASSOCIATED PROTEIN OF 70 KDA, NA/PI COTRANSPORTER C-TERMINAL-ASSOCIATED PROTEIN, NAPI-CAP1, NA(+)/H(+) EXCHANGER REGULATORY FACTOR 3, SODIUM-HYDROGEN EXCHANGER REGULATORY FACTOR 3

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2EEJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.NHRF3_HUMAN9-90
134-215
243-323
378-458
  1-
-
-
A:10-90

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENST000003447703ENSE00001411267chr1:145743263-14574333371NHRF3_HUMAN-00--
1.4bENST000003447704bENSE00001372163chr1:145747042-145747253212NHRF3_HUMAN1-70700--
1.5ENST000003447705ENSE00001759427chr1:145748338-145748587250NHRF3_HUMAN71-154840--
1.6ENST000003447706ENSE00001710717chr1:145752428-145752564137NHRF3_HUMAN154-199460--
1.7ENST000003447707ENSE00002188888chr1:145753955-145754150196NHRF3_HUMAN200-265661A:1-22
1.8ENST000003447708ENSE00001787521chr1:145756417-145756613197NHRF3_HUMAN265-330661A:3-7 (gaps)21
1.9aENST000003447709aENSE00001784849chr1:145761178-145761402225NHRF3_HUMAN331-405751A:8-3730
1.10aENST0000034477010aENSE00001706980chr1:145762039-145762329291NHRF3_HUMAN406-502971A:38-96 (gaps)82
1.12dENST0000034477012dENSE00001365469chr1:145763570-145764074505NHRF3_HUMAN503-519170--

(-) 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:96
 aligned with NHRF3_HUMAN | Q5T2W1 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:228
                                   269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479        
          NHRF3_HUMAN   260 GSEQKGQIIKDIDSGSPAEEAGLKNNDLVVAVNGESVETLDHDSVVEMIRKGGDQTSLLVVDKETDNMYRLAHFSPFLYYQSQELPNGSVKEAPAPTPTSLEVSSPPDTTEEVDHKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCGKKAYDYFQAKKIPIVSSLADPLDTPPDSKEG 487
               SCOP domains d2           eej                a_                                                                                   A: automated matches                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-----------...----------------..----------------------------------------------------------------------------------.eeeeee........ee........eeee.....hhhhhhh.....ee.ee........hhhhhhhhhhhhh.eeeeee.....---------------------....--. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE PDZ  PDB: - UniProt: 243-323                                    ------------------------------------------------------PDZ  PDB: A:10-90 UniProt: 378-458                                               ----------------------------- PROSITE
           Transcript 1 (1) 1.7   -----------------------------------------------------------------Exon 1.9a  PDB: A:8-37 UniProt: 331-405 [INCOMPLETE]                       Exon 1.10a  PDB: A:38-96 (gaps) UniProt: 406-502 [INCOMPLETE]                      Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.8  PDB: A:3-7 (gaps) UniProt: 265-330 [INCOMPLETE]         ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2eej A   1 GS-----------SGS----------------SG----------------------------------------------------------------------------------PKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCGKKS---------------------GPSS--G  96
                             |       -   | |   -         -  ||     -         -         -         -         -         -         -         -      | 11        21        31        41        51        61        71        81        91         -         - |  |  |
                             2           3 5                6|                                                                                  8                                                                                 91                    92 95 96
                                                             7                                                                                                                                                                                                  

   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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (NHRF3_HUMAN | Q5T2W1)
molecular function
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005124    scavenger receptor binding    Interacting selectively and non-covalently with scavenger receptors, a family of proteins that are expressed on myeloid cells and are involved in the uptake of effete cellular components and foreign particles.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0015879    carnitine transport    The directed movement of carnitine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carnitine is a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0015893    drug transport    The directed movement of a drug, a substance used in the diagnosis, treatment or prevention of a disease, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0034767    positive regulation of ion transmembrane transport    Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    GO:0090314    positive regulation of protein targeting to membrane    Any process that increases the frequency, rate or extent of the process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:0044070    regulation of anion transport    Any process that modulates the frequency, rate or extent of the directed movement of anions, atoms or small molecules with a net negative charge into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0031526    brush border membrane    The portion of the plasma membrane surrounding the brush border.
    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:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0031528    microvillus membrane    The portion of the plasma membrane surrounding a microvillus.
    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)

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        NHRF3_HUMAN | Q5T2W12eei 2vsp 3tmh 4q2p

(-) Related Entries Specified in the PDB File

2eei DIFFERENT DOMAIN OF THE SAME PROTEIN RELATED ID: HSS001001614.3 RELATED DB: TARGETDB