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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE HUMAN ALPHA9 NICOTINIC ACETYLCHOLINE RECEPTOR
 
Authors :  P. Giastas, M. Zouridakis, E. Zarkadas, S. J. Tzartos
Date :  23 Apr 14  (Deposition) - 01 Oct 14  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Signaling Protein, Ligand Binding Domain, Cys-Loop Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Zouridakis, P. Giastas, E. Zarkadas, D. Chroni-Tzartou, P. Bregestovski, S. J. Tzartos
Crystal Structures Of Free And Antagonist-Bound States Of Human Alpha9 Nicotinic Receptor Extracellular Domain
Nat. Struct. Mol. Biol. V. 21 976 2014
PubMed-ID: 25282151  |  Reference-DOI: 10.1038/NSMB.2900

(-) Compounds

Molecule 1 - NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9
    ChainsA
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System PlasmidPPICZAA
    Expression System StrainX33
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR DOMAIN, RESIDUES 26-237
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNICOTINIC ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9, NACHR ALPHA-9, HUMAN ALPHA9 NICOTINIC ACETYLCHOLINE RECEPTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:55 , HOH A:2201BINDING SITE FOR RESIDUE EDO A1218
2AC2SOFTWAREASN A:96 , ASN A:145 , THR A:147 , NAG A:1217 , HOH A:2187 , HOH A:2202 , HOH A:2203BINDING SITE FOR RESIDUE EDO A1219
3AC3SOFTWARETYR A:199 , HOH A:2204 , HOH A:2205BINDING SITE FOR RESIDUE EDO A1220
4AC4SOFTWAREHOH A:2125BINDING SITE FOR RESIDUE EDO A1221
5AC5SOFTWAREVAL A:30 , ASN A:32 , ARG A:48 , HOH A:2041BINDING SITE FOR MONO-SACCHARIDE NAG A1216 BOUND TO ASN A 32
6AC6SOFTWAREGLN A:143 , ASN A:145 , VAL A:186 , ASN A:188 , THR A:203 , THR A:205 , EDO A:1219 , HOH A:2176 , HOH A:2187 , HOH A:2198 , HOH A:2200BINDING SITE FOR MONO-SACCHARIDE NAG A1217 BOUND TO ASN A 145

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:130 -A:144
2A:194 -A:195

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:100 -Glu A:101
2Phe A:137 -Pro A:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_031151R96QACHA9_HUMANPolymorphism10024518AR71Q

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEUROTR_ION_CHANNELPS00236 Neurotransmitter-gated ion-channels signature.ACHA9_HUMAN155-169  1A:130-144

(-) Exons   (0, 0)

(no "Exon" information available for 4D01)

(-) 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:212
 aligned with ACHA9_HUMAN | Q9UGM1 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:214
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236    
          ACHA9_HUMAN    27 DGKYAQKLFNDLFEDYSNALRPVEDTDKVLNVTLQITLSQIKDMDERNQILTAYLWIRQIWHDAYLTWDRDQYDGLDSIRIPSDLVWRPDIVLYNKADDESSEPVNTNVVLRYDGLITWDAPAITKSSCVVDVTYFPFDNQQCNLTFGSWTYNGNQVDIFNALDSGDLSDFIEDVEWEVHGMPAVKNVISYGCCSEPYPDVTFTLLLKRRSSFY 240
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh................eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.hhhhhh...eeeee.hhh....eee.......--.....eeeee.eeeeeeeeeeeeeeeeeee.......eeeeeeeeee.......eeeee...............eeeee..eeeeeee......eeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------NEUROTR_ION_CHA----------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d01 A   2 DGKYAQKLFNDLFEDYSNALRPVEDTDKVLNVTLQITLSQIKDMDERNQILTAYLWIRQIWHDAYLTWDRDQYDGLDSIRIPSDLVWRPDIVLYNKADDE--EPVNTNVVLRYDGLITWDAPAITKSSCVVDVTYFPFDNQQCNLTFGSWTYNGNQVDIFNALDSGDLSDFIEDVEWEVHGMPAVKNVISYGCCSEPYPDVTFTLLLKRRSHHH 215
                                    11        21        31        41        51        61        71        81        91       101  |    111       121       131       141       151       161       171       181       191       201       211    
                                                                                                                             101  |                                                                                                               
                                                                                                                                104                                                                                                               

   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 4D01)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D01)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D01)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ACHA9_HUMAN | Q9UGM1)
molecular function
    GO:0042166    acetylcholine binding    Interacting selectively and non-covalently with acetylcholine, an acetic acid ester of the organic base choline that functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions.
    GO:0022848    acetylcholine-gated cation-selective channel activity    Selectively enables the transmembrane transfer of a cation by a channel that opens upon binding acetylcholine.
    GO:0005262    calcium channel activity    Enables the facilitated diffusion of a calcium ion (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:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    GO:0015276    ligand-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.
biological process
    GO:0070588    calcium ion transmembrane transport    A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006816    calcium ion transport    The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0098655    cation transmembrane transport    A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006812    cation transport    The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0099565    chemical synaptic transmission, postsynaptic    The part of synaptic transmission occurring in the post-synapse: a signal transduction pathway consisting of neurotransmitter receptor activation and its effects on postsynaptic membrane potential and the ionic composition of the postsynaptic cytosol.
    GO:0050910    detection of mechanical stimulus involved in sensory perception of sound    The series of events involved in the perception of sound vibration in which the vibration is received and converted into a molecular signal.
    GO:0042472    inner ear morphogenesis    The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
    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:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007271    synaptic transmission, cholinergic    The vesicular release of acetylcholine from a presynapse, across a chemical synapse, the subsequent activation of dopamine 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.
cellular component
    GO:0005892    acetylcholine-gated channel complex    A homo- or hetero-pentameric protein complex that forms a transmembrane channel through which ions may pass in response to acetylcholine binding.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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

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

UniProtKB/Swiss-Prot
        ACHA9_HUMAN | Q9UGM14uxu 4uy2

(-) Related Entries Specified in the PDB File

4uxu CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE HUMAN ALPHA9 NICOTINIC ACETYLCHOLINE RECEPTOR IN COMPLEX WITH METHYLLYCACONITINE
4uy2 CRYSTAL STRUCTURE OF THE COMPLEX OF THE EXTRACELLULAR DOMAIN OF HUMAN ALPHA9 NACHR WITH ALPHA-BUNGAROTOXIN.