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(-) Description

Title :  THE THIRD PDZ DOMAIN FROM THE SYNAPTIC PROTEIN PSD-95
 
Authors :  D. A. Doyle, A. Lee, J. Lewis, E. Kim, M. Sheng, R. Mackinnon
Date :  20 May 98  (Deposition) - 21 Oct 98  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptide Recognition, Protein Localization (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. A. Doyle, A. Lee, J. Lewis, E. Kim, M. Sheng, R. Mackinnon
Crystal Structures Of A Complexed And Peptide-Free Membrane Protein-Binding Domain: Molecular Basis Of Peptide Recognition By Pdz.
Cell(Cambridge, Mass. ) V. 85 1067 1996
PubMed-ID: 8674113  |  Reference-DOI: 10.1016/S0092-8674(00)81307-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PSD-95
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-4T-1
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentTHE THIRD PDZ DOMAIN OF PSD-95
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 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 1BFE)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1PEPUNKNOWNGLY A:322 , LEU A:323 , GLY A:324 , PHE A:325 , ASN A:326 , ILE A:327 , SER A:339 , HIS A:372 , LEU A:379RESIDUES INVOLVED IN THE BINDING OF THE FOUR C- TERMINAL RESIDUES OF CRIPT.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DLG4_RAT65-152
160-247
313-394
  1-
-
A:313-394
2SH3PS50002 Src homology 3 (SH3) domain profile.DLG4_RAT428-498  1A:405-408

(-) Exons   (0, 0)

(no "Exon" information available for 1BFE)

(-) 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:110
 aligned with DLG4_RAT | P31016 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:223
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525   
             DLG4_RAT   306 DIPREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRFEAKIHDLREQLMNSSLGSGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDAGDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYETVTQ 528
               SCOP domains d1bfea_ A: Synaptic protein PSD-95                                                                                                                                                                                              SCOP domains
               CATH domains 1bfeA00 A:306-415  [code=2.30.42.10, no name defined]                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.......eeeee......eeeeee....hhhhh......eeeeee.........hhhhhhhhhh...eeeeeeee.hhhhh....----------.e------------------------------------------------------------ee...-----------------------------------..--------eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PDZ  PDB: A:313-394 UniProt: 313-394                                              ---------------------------------SH3  PDB: A:405-408 UniProt: 428-498                                   ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bfe A 306 DIPREPRRIVIHRGSTGLGFNIIGGEDGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRFEA----------NS------------------------------------------------------------RVNSS-----------------------------------GR--------IVTN 415
                                   315       325       335       345       355       365       375       385       395      |  -       ||-         -         -         -         -         -       405   |     -         -         -       410|      412   
                                                                                                                          402        403|                                                          405 409                                 410|      412   
                                                                                                                                      404                                                                                                   411            

   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  (0, 0)

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

(-) Gene Ontology  (60, 60)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DLG4_RAT | P31016)
molecular function
    GO:0031748    D1 dopamine receptor binding    Interacting selectively and non-covalently with a D1 dopamine receptor.
    GO:0031812    P2Y1 nucleotide receptor binding    Interacting selectively and non-covalently with a P2Y1 nucleotide receptor.
    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:0033130    acetylcholine receptor binding    Interacting selectively and non-covalently with an acetylcholine receptor.
    GO:0031697    beta-1 adrenergic receptor binding    Interacting selectively and non-covalently with a beta-1 adrenergic receptor.
    GO:0035254    glutamate receptor binding    Interacting selectively and non-covalently with a glutamate receptor.
    GO:0004385    guanylate kinase activity    Catalysis of the reaction: ATP + GMP = ADP + GDP.
    GO:0035255    ionotropic glutamate receptor binding    Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels.
    GO:0097109    neuroligin family protein binding    Interacting selectively and non-covalently with a member of the neuroligin protein family, neuronal cell surface proteins that mediate synapse formation.
    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: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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    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.
    GO:0097110    scaffold protein binding    Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
biological process
    GO:0097113    AMPA glutamate receptor clustering    The glutamate receptor clustering process in which alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptors are localized to distinct domains in the cell membrane.
    GO:0046710    GDP metabolic process    The chemical reactions and pathways involving GDP, guanosine 5'-diphosphate.
    GO:0046037    GMP metabolic process    The chemical reactions and pathways involving GMP, guanosine monophosphate.
    GO:0060997    dendritic spine morphogenesis    The process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0045184    establishment of protein localization    The directed movement of a protein to a specific location.
    GO:0045197    establishment or maintenance of epithelial cell apical/basal polarity    Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of an epithelial cell.
    GO:0035641    locomotory exploration behavior    The specific movement from place to place of an organism in response to a novel environment.
    GO:0002091    negative regulation of receptor internalization    Any process that stops, prevents, or reduces the frequency, rate or extent of receptor internalization.
    GO:0050885    neuromuscular process controlling balance    Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors.
    GO:0045161    neuronal ion channel clustering    The process in which voltage-gated ion channels become localized to distinct subcellular domains in the neuron. Specific targeting, clustering, and maintenance of these channels in their respective domains are essential to achieve high conduction velocities of action potential propagation.
    GO:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:2000463    positive regulation of excitatory postsynaptic potential    Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
    GO:0050806    positive regulation of synaptic transmission    Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0035418    protein localization to synapse    Any process in which a protein is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
    GO:0097120    receptor localization to synapse    Any process in which a receptor is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
    GO:2000310    regulation of NMDA receptor activity    Any process that modulates the frequency, rate or extent of N-methyl-D-aspartate selective glutamate receptor activity.
    GO:2000821    regulation of grooming behavior    Any process that modulates the frequency, rate or extent of grooming behavior.
    GO:0048169    regulation of long-term neuronal synaptic plasticity    A process that modulates long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
    GO:0035176    social behavior    Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
    GO:0016188    synaptic vesicle maturation    Steps required to form an initiated synaptic vesicle into a fully formed and transmissible synaptic vesicle.
    GO:0071625    vocalization behavior    The behavior in which an organism produces sounds by a mechanism involving its respiratory system.
cellular component
    GO:0032281    AMPA glutamate receptor complex    An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. The AMPA receptors mediate fast synaptic transmission in the CNS and are composed of subunits GluR1-4, products from separate genes. These subunits have an extracellular N-terminus and an intracellular C-terminus.
    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:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0032839    dendrite cytoplasm    All of the contents of a dendrite, excluding the surrounding plasma membrane.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    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:0060076    excitatory synapse    A synapse in which an action potential in the presynaptic cell increases the probability of an action potential occurring in the postsynaptic cell.
    GO:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    GO:0008328    ionotropic glutamate receptor complex    A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex.
    GO:0044224    juxtaparanode region of axon    A region of an axon near a node of Ranvier that is between the paranode and internode regions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0044306    neuron projection terminus    The specialized, terminal region of a neuron projection such as an axon or a dendrite.
    GO:0044309    neuron spine    A small membranous protrusion, often ending in a bulbous head and attached to the neuron by a narrow stalk or neck.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    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:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        DLG4_RAT | P310161be9 1iu0 1iu2 1jxm 1jxo 1kjw 1qlc 1rgr 1tp3 1tp5 1tq3 2ka9 2mho 2xkx 3gsl 3wp0 3wp1 5b64 5d13 5hdy 5heb 5hed 5het 5hey 5hf1 5hf4 5hfb 5hfc 5hfd 5hfe 5hff

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BFE)