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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF THE CALCIUM-FREE PICCOLO C2A-DOMAIN
 
Authors :  J. Garcia, S. H. Gerber, S. Sugita, T. C. Sudhof, J. Rizo
Date :  14 Nov 03  (Deposition) - 13 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Beta-Sandwich, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Garcia, S. H. Gerber, S. Sugita, T. C. Sudhof, J. Rizo
A Conformational Switch In The Piccolo C2A Domain Regulated By Alternative Splicing.
Nat. Struct. Mol. Biol. V. 11 45 2004
PubMed-ID: 14718922  |  Reference-DOI: 10.1038/NSMB707
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PICCOLO PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-KG
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC2A-DOMAIN
    GenePCLO
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymMULTIDOMAIN PRESYNAPTIC CYTOMATRIX PROTEIN

 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 1RH8)

(-) Sites  (0, 0)

(no "Site" information available for 1RH8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RH8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RH8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RH8)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.PCLO_RAT4653-4752
4968-5059
  1A:4653-4752
-

(-) Exons   (0, 0)

(no "Exon" information available for 1RH8)

(-) 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:142
 aligned with PCLO_RAT | Q9JKS6 from UniProtKB/Swiss-Prot  Length:5085

    Alignment length:142
                                  4644      4654      4664      4674      4684      4694      4704      4714      4724      4734      4744      4754      4764      4774  
            PCLO_RAT   4635 ASHPITGEIQLQINYDLGNLIIHILQARNLVPRDNNGYSDPFVKVYLLPGRGQVMVVQNASAEYKRRTKYVQKSLNPEWNQTVIYKSISMEQLMKKTLEVTVWDYDRFSSNDFLGEVLIDLSSTSHLDNTPRWYPLKEQTES 4776
               SCOP domains d1rh8a_ A: Piccolo                                                                                                                             SCOP domains
               CATH domains 1rh8A00 A:4635-4776 C2- domain Calcium/lipid binding domain                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee..eeeeeeeeee.............eeeeee.......ee....hhhhhh....hhhhhh.eeeeeeee...hhhhhh..eeeeeeeee.....eeeeeeeeee...hhhhh...eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------C2  PDB: A:4653-4752 UniProt: 4653-4752                                                             ------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rh8 A 4635 ASHPITGEIQLQINYDLGNLIIHILQARNLVPRDNNGYSDPFVKVYLLPGRGQVMVVQNASAEYKRRTKYVQKSLNPEWNQTVIYKSISMEQLMKKTLEVTVWDYDRFSSNDFLGEVLIDLSSTSHLDNTPRWYPLKEQTES 4776
                                  4644      4654      4664      4674      4684      4694      4704      4714      4724      4734      4744      4754      4764      4774  

   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
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1RH8)

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (PCLO_RAT | Q9JKS6)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005544    calcium-dependent phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005522    profilin binding    Interacting selectively and non-covalently with profilin, an actin-binding protein that forms a complex with G-actin and prevents it from polymerizing to form F-actin.
    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:0001222    transcription corepressor binding    Interacting selectively and non-covalently with a transcription corepressor, any protein involved in negative regulation of transcription via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0007416    synapse assembly    The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
    GO:0016080    synaptic vesicle targeting    The process in which synaptic vesicles are directed to specific destination membranes, mediated by molecules at the vesicle membrane and target membrane surfaces.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0044316    cone cell pedicle    A specialized axon terminus which is produced by retinal cone cells. Pedicles are large, conical, flat end-feet (8-10 micrometers diameter) of the retinal cone axon that lie more or less side by side on the same plane at the outer edge of the outer plexiform layer (OPL).
    GO:0048788    cytoskeleton of presynaptic active zone    The specialized cytoskeletal matrix of the presynaptic active zone. It has specialized functions in organizing synaptic events such as immobilisation or translocation of synaptic vesicles, and assembling active zone components. It is believed to form a molecular scaffold that organizes neurotransmitter release sites.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0060077    inhibitory synapse    A synapse in which an action potential in the presynaptic cell reduces the probability of an action potential occurring in the postsynaptic cell.
    GO:0031594    neuromuscular junction    The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0048786    presynaptic active zone    A specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, and a specialized cortical cytoskeletal matrix.
    GO:0097470    ribbon synapse    Type of synapse characterized by an electron-dense ribbon, lamella (bar) or spherical body in the presynaptic process cytoplasm.
    GO:0044317    rod spherule    A specialized neuron projection which is the site of synaptic transmission produced by retinal rod cells. Rod spherules are small round enlargements of the axon (3-5 micrometers diameter) or even extensions of the cell body.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0043195    terminal bouton    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.
    GO:0030133    transport vesicle    Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

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