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(-) Description

Title :  SECOND AND THIRD TRANSMEMBRANE DOMAINS OF THE ALPHA-1 SUBUNIT OF HUMAN GLYCINE RECEPTOR
 
Authors :  D. Ma, Z. Liu, L. Li, P. Tang, Y. Xu
Date :  20 Jul 05  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Glycine Receptor, Nmr, Second Transmembrane Domain, Third Transmembrane Domain, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Ma, Z. Liu, L. Li, P. Tang, Y. Xu
Structure And Dynamics Of The Second And Third Transmembrane Domains Of Human Glycine Receptor.
Biochemistry V. 44 8790 2005
PubMed-ID: 15952785  |  Reference-DOI: 10.1021/BI050256N
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCINE RECEPTOR ALPHA-1 CHAIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPLYSS
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentSECOND AND THIRD TRANSMEMBRANE DOMAINS
    GeneGLRA1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGLYCINE RECEPTOR 48 KDA SUBUNIT, STRYCHNINE BINDING SUBUNIT

 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 1VRY)

(-) Sites  (0, 0)

(no "Site" information available for 1VRY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

NMR Structure (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_010112P278TGLRA1_HUMANDisease (HKPX1)121918413AP-2T
2UniProtVAR_010113R280HGLRA1_HUMANDisease (HKPX1)281864918AR0H
3UniProtVAR_000297Q294HGLRA1_HUMANDisease (HKPX1)121918411AQ14H
4UniProtVAR_000298R299LGLRA1_HUMANDisease (HKPX1)121918408AR19L
5UniProtVAR_000299R299QGLRA1_HUMANDisease (HKPX1)121918408AR19Q
6UniProtVAR_000300K304EGLRA1_HUMANDisease (HKPX1)121918412AK24E
7UniProtVAR_000301Y307CGLRA1_HUMANDisease (HKPX1)121918410AY27C
8UniProtVAR_075423V308MGLRA1_HUMANDisease (HKPX1)  ---AV28M
9UniProtVAR_075424L319PGLRA1_HUMANDisease (HKPX1)  ---AL39P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VRY)

(-) Exons   (0, 0)

(no "Exon" information available for 1VRY)

(-) 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:61
 aligned with GLRA1_HUMAN | P23415 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:61
                                   286       296       306       316       326       336 
          GLRA1_HUMAN   277 APARVGLGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFVSR 337
               SCOP domains ----d1vrya1 A:1-57 Glycine receptor alpha-1 chain             SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -T-H-------------H----L----E--CM----------P------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------Q-------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 1vry A  -3 LPARVGLGITTVLTLTTQSSGSRASLPKVSYVKAIDIWLAVCLLFVFSALLEYAAVNFVSR  57
                                     6        16        26        36        46        56 

   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
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VRY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (58, 58)

NMR Structure(hide GO term definitions)
Chain A   (GLRA1_HUMAN | P23415)
molecular function
    GO:0005254    chloride channel activity    Enables the facilitated diffusion of a chloride (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    GO:0005230    extracellular ligand-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts.
    GO:0016934    extracellular-glycine-gated chloride channel activity    Enables the transmembrane transfer of a chloride ion by a channel that opens when extracellular glycine has been bound by the channel complex or one of its constituent parts.
    GO:0016933    extracellular-glycine-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when extracellular glycine has been bound by the channel complex or one of its constituent parts.
    GO:0016594    glycine binding    Interacting selectively and non-covalently with glycine, aminoethanoic acid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0030977    taurine binding    Interacting selectively and non-covalently with taurine.
    GO:0022824    transmitter-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when a specific neurotransmitter has been bound by the channel complex or one of its constituent parts.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007340    acrosome reaction    The discharge, by sperm, of a single, anterior secretory granule following the sperm's attachment to the zona pellucida surrounding the oocyte. The process begins with the fusion of the outer acrosomal membrane with the sperm plasma membrane and ends with the exocytosis of the acrosomal contents into the egg.
    GO:0001508    action potential    A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
    GO:0007628    adult walking behavior    The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
    GO:0006820    anion transport    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:0071230    cellular response to amino acid stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0071361    cellular response to ethanol    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
    GO:0071294    cellular response to zinc ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:1902476    chloride transmembrane transport    The directed movement of chloride across a membrane.
    GO:0006821    chloride transport    The directed movement of chloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0060080    inhibitory postsynaptic potential    A process that causes a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    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:0006936    muscle contraction    A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
    GO:0051970    negative regulation of transmission of nerve impulse    Any process that stops, prevents, or reduces the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation.
    GO:0050905    neuromuscular process    Any process pertaining to the functions of the nervous and muscular systems of an organism.
    GO:0050884    neuromuscular process controlling posture    Any process in which an organism voluntarily modulates its posture, the alignment of its anatomical parts.
    GO:0007218    neuropeptide signaling pathway    The series of molecular signals generated as a consequence of a peptide neurotransmitter binding to a cell surface receptor.
    GO:2000344    positive regulation of acrosome reaction    Any process that activates or increases the frequency, rate or extent of the acrosome reaction.
    GO:0051291    protein heterooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0042391    regulation of membrane potential    Any process that modulates the 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:0043576    regulation of respiratory gaseous exchange    Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment.
    GO:0002087    regulation of respiratory gaseous exchange by neurological system process    A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates.
    GO:0097305    response to alcohol    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 an alcohol stimulus.
    GO:0060013    righting reflex    A reflex process in which an animal immediately tries to turn over after being placed in a supine position.
    GO:0001964    startle response    An action or movement due to the application of a sudden unexpected stimulus.
    GO:0060012    synaptic transmission, glycinergic    The vesicular release of glycine from a presynapse, across a chemical synapse, the subsequent activation of glycine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    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.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    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:0034707    chloride channel complex    An ion channel complex through which chloride ions pass.
    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: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:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    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: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.

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 Related Entries

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        GLRA1_HUMAN | P234151mot 2m6b 2m6i 4x5t

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