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(-) Description

Title :  NMR STRUCTURE OF DREAM
 
Authors :  J. Ames
Date :  30 Aug 07  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Ef-Hand, Calcium, Lxxll, Dna Binding Protein, Dimer, Alternative Splicing, Apoptosis, Cytoplasm, Endoplasmic Reticulum, Golgi Apparatus, Ion Transport, Ionic Channel, Lipoprotein, Membrane, Nucleus, Palmitate, Polymorphism, Potassium, Potassium Channel, Potassium Transport, Repressor, Transcription, Transcription Regulation, Transport, Voltage-Gated Channel (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. D. Lusin, M. Vanarotti, C. Li, A. Valiveti, J. B. Ames
Nmr Structure Of Dream: Implications For Ca(2+)-Dependent Dna Binding And Protein Dimerization.
Biochemistry V. 47 2252 2008
PubMed-ID: 18201103  |  Reference-DOI: 10.1021/BI7017267
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CALSENILIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET23A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneKCNIP3, CSEN, DREAM, KCHIP3
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymKV CHANNEL-INTERACTING PROTEIN 3, KCHIP3, A-TYPE POTASSIUM CHANNEL MODULATORY PROTEIN 3, DRE-ANTAGONIST MODULATOR, DREAM

 Structural Features

(-) Chains, Units

  
NMR Structure (15x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:175 , ASN A:177 , THR A:183BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREMET A:222 , ASP A:223 , ARG A:224BINDING SITE FOR RESIDUE CA A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 5)

NMR Structure (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CSEN_MOUSE126-161
162-197
210-245
  3A:126-161
A:162-197
A:210-245
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CSEN_MOUSE175-187
223-235
  2A:175-187
A:223-235

(-) Exons   (0, 0)

(no "Exon" information available for 2JUL)

(-) 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:181
 aligned with CSEN_MOUSE | Q9QXT8 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:181
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255 
           CSEN_MOUSE    76 PEGLDQLQAQTKFTKKELQSLYRGFKNECPTGLVDEDTFKLIYSQFFPQGDATTYAHFLFNAFDADGNGAIHFEDFVVGLSILLRGTVHEKLKWAFNLYDINKDGCITKEEMLAIMKSIYDMMGRHTYPILREDAPLEHVERFFQKMDRNQDGVVTIDEFLETCQKDENIMNSMQLFENVI 256
               SCOP domains d2jula_ A: automated matches                                                                                                                                                          SCOP domains
               CATH domains 2julA00 A:76-256 EF-hand                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..hhhhhhhhhhhhhhhh....eehhhhhhhhhhhh....hhhhhhhhhhhh......ee.hhhhhhhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------EF_HAND_2  PDB: A:126-161           EF_HAND_2  PDB: A:162-197           ------------EF_HAND_2  PDB: A:210-245           ----------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------EF_HAND_1    -----------------------------------EF_HAND_1    --------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jul A  76 PEGLDQLQAQTKFTKKELQSLYRGFKNECPTGLVDEDTFKLIYSQFFPQGDATTYAHFLFNAFDADGNGAIHFEDFVVGLSILLRGTVHEKLKWAFNLYDINKDGCITKEEMLAIMKSIYDMMGRHTYPILREDAPLEHVERFFQKMDRNQDGVVTIDEFLETCQKDENIMNSMQLFENVI 256
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255 

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

NMR Structure(hide GO term definitions)
Chain A   (CSEN_MOUSE | Q9QXT8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005267    potassium channel activity    Enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0015459    potassium channel regulator activity    Modulates potassium channel activity via direct interaction interaction with a potassium channel (binding or modification).
    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:0005244    voltage-gated ion channel activity    Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0048266    behavioral response to pain    Any process that results in a change in the behavior of an organism as a result of a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0071805    potassium ion transmembrane transport    A process in which a potassium ion is transported from one side of a membrane to the other.
    GO:0006813    potassium ion transport    The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0072659    protein localization to plasma membrane    A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
    GO:0034765    regulation of ion transmembrane transport    Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    GO:0043523    regulation of neuron apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons.
    GO:1901379    regulation of potassium ion transmembrane transport    Any process that modulates the frequency, rate or extent of potassium ion transmembrane transport.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048265    response to pain    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 a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    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:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    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: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: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:0008076    voltage-gated potassium channel complex    A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

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