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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE FIRST PDZ DOMAIN OF HUMAN NHERF-2 (SLC9A3R2)
 
Authors :  E. Papagrigoriou, C. Phillips, C. Gileadi, J. Elkins, E. Salah, G. Berridge, P. Savitsky, F. Gorrec, C. Umeano, E. Ugochukwu, O. Gileadi, N. Burgess, A. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, D. A. Doyle, Structural Genomics Consortium (Sgc)
Date :  21 Dec 06  (Deposition) - 16 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Protein, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Papagrigoriou, C. Phillips, C. Gileadi, J. Elkins, E. Salah, G. Berridge, P. Savitsky, F. Gorrec, C. Umeano, E. Ugochukwu, O. Gileadi, N. Burgess, A. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, D. A. Doyle
The Crystal Structure Of The First Pdz Domain Of Human Nherf-2 (Slc9A3R2)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NA(+)/H(+) EXCHANGE REGULATORY COFACTOR NHE-RF2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneSLC9A3R2, NHERF2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNHERF-2, TYROSINE KINASE ACTIVATOR PROTEIN 1, TKA- 1, SRY-INTERACTING PROTEIN 1, SIP-1, SOLUTE CARRIER FAMILY 9 ISOFORM A3 REGULATORY FACTOR 2, NHE3 KINASE A REGULATORY PROTEIN E3KARP, SODIUM-HYDROGEN EXCHANGER REGULATORY FACTOR 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SCN1Ligand/IonTHIOCYANATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:25 , ARG A:36BINDING SITE FOR RESIDUE SCN A 5712
2AC2SOFTWAREASN A:59 , GLN A:81 , ARG A:83 , HOH A:5743 , HOH A:5753BINDING SITE FOR RESIDUE EDO A 2762

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.NHRF2_HUMAN11-91
151-231
  1A:10-90
-

(-) Exons   (0, 0)

(no "Exon" information available for 2OCS)

(-) 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:85
 aligned with NHRF2_HUMAN | Q15599 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:89
                                    17        27        37        47        57        67        77        87         
           NHRF2_HUMAN    8 RPRLCRLVRGEQGYGFHLHGEKGRRGQFIRRVEPGSPAEAAALRAGDRLVEVNGVNVEGETHHQVVQRIKAVEGQTRLLVVDQETDEEL 96
               SCOP domains d2ocsa_ A: automated    matches                                                           SCOP domains
               CATH domains 2ocsA00 A:7-94  [code   =2.30.42.10, no name defined]                                     CATH domains
               Pfam domains ---PDZ-2ocsA01 A:10-8   7                                                        --- ---- Pfam domains
         Sec.struct. author ..eeeeee.......eeeee.---..eeeeee...hhhhhh.....eeeeee..ee....hhhhhhhhhhh...eeeeeeee..-.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: A:10-90 UniProt: 11-91                                                 ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  2ocs A  7 MPRLCRLVRGEQGYGFHLHGE---RGQFIRRVEPGSPAEAAALRAGDRLVEVNGVNVEGETHHQVVQRIKAVEGQTRLLVVDQE-DTSV 94
                                    16        26|   |   36        46        56        66        76        86   | |   
                                               27  31                                                         90 |   
                                                                                                                91   

   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PDZ-like (184)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NHRF2_HUMAN | Q15599)
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:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0016247    channel regulator activity    Modulates the activity of a channel. A channel catalyzes energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel.
    GO:0050750    low-density lipoprotein particle receptor binding    Interacting selectively and non-covalently with a low-density lipoprotein receptor.
    GO:0019902    phosphatase binding    Interacting selectively and non-covalently with any phosphatase.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0032947    protein complex scaffold activity    A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0048839    inner ear development    The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
    GO:0045838    positive regulation of membrane potential    Any process that activates or increases the frequency, rate or extent of establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NHRF2_HUMAN | Q155992d11 2he4 4p0c

(-) Related Entries Specified in the PDB File

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