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(-) Description

Title :  X-RAY STRUCTURE OF THE PENTAMERIC LIGAND GATED ION CHANNEL OF GLOEBACTER VIOLACEUS (GLIC) IN A PRESUMPTIVE OPEN CONFORMATION
 
Authors :  R. J. C. Hilf, R. Dutzler
Date :  15 Sep 08  (Deposition) - 11 Nov 08  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Pentameric Ligand Gated Ion Channel, Membrane Protein, Prokaryotic Cys-Loop Receptor, Cation Selective Channel (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. J. Hilf, R. Dutzler
Structure Of A Potentially Open State Of A Proton-Activated Pentameric Ligand-Gated Ion Channel
Nature V. 457 115 2008
PubMed-ID: 18987630  |  Reference-DOI: 10.1038/NATURE07461
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLR4197 PROTEIN
    ChainsA, B, C, D, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET26
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 50-359
    Organism ScientificGLOEOBACTER VIOLACEUS
    Organism Taxid33072
    StrainPCC 7421

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3EHZ)

(-) Sites  (0, 0)

(no "Site" information available for 3EHZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EHZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EHZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EHZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EHZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3EHZ)

(-) 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:310
 aligned with GLIC_GLOVI | Q7NDN8 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:310
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
           GLIC_GLOVI    50 PPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF 359
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ehzA01 A:7-195  [code=2.70.170.10, no name defined]                                                                                                                                         3ehzA02 A:196-316 Glr4197 protein                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.eeeeeeeeee....eeeeeeeeeeeee.hhhh..........ee..........ee........eeeeeeeee....eeeeeeeeeeeee...hhhhhhh.eeeeee..eee.....eeeee.hhhh...........eeeeeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ehz A   7 PPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF 316
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with GLIC_GLOVI | Q7NDN8 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:310
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
           GLIC_GLOVI    50 PPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF 359
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ehzB01 B:7-195  [code=2.70.170.10, no name defined]                                                                                                                                         3ehzB02 B:196-316 Glr4197 protein                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.eeeeeeeeee....eeeeeeeeeeeee.hhhh..........ee..........ee........eeeeeeeee....eeeeeeeeeeeee...hhhhhhh.eeeeee..eee.....eeeee................eeeeeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ehz B   7 PPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF 316
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316

Chain C from PDB  Type:PROTEIN  Length:310
 aligned with GLIC_GLOVI | Q7NDN8 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:310
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
           GLIC_GLOVI    50 PPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF 359
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ehzC01 C:7-195  [code=2.70.170.10, no name defined]                                                                                                                                         3ehzC02 C:196-316 Glr4197 protein                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.eeeeeeeeee....eeeeeeeeeeeee.hhhh..........ee..........ee........eeeeeeeee....eeeeeeeeeeeee...hhhhhhh.eeeeee..ee......eeeee................eeeeeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ehz C   7 PPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF 316
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316

Chain D from PDB  Type:PROTEIN  Length:310
 aligned with GLIC_GLOVI | Q7NDN8 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:310
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
           GLIC_GLOVI    50 PPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF 359
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ehzD01 D:7-195  [code=2.70.170.10, no name defined]                                                                                                                                         3ehzD02 D:196-316 Glr4197 protein                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.eeeeeeeeee....eeeeeeeeeeeee.hhhh..........ee..........ee........eeeeeeeee....eeeeeeeeeeeee...hhhhhhh.eeeeee..eee.....eeeee.hhhh...........eeeeeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ehz D   7 PPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF 316
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316

Chain E from PDB  Type:PROTEIN  Length:310
 aligned with GLIC_GLOVI | Q7NDN8 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:310
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
           GLIC_GLOVI    50 PPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF 359
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ehzE01 E:7-195  [code=2.70.170.10, no name defined]                                                                                                                                         3ehzE02 E:196-316 Glr4197 protein                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.eeeeeeeeee....eeeeeeeeeeeee.hhhh..........ee..........ee........eeeeeeeee....eeeeeeeeeeeee...hhhhhhh.eeeeee..ee......eeeee................eeeeeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ehz E   7 PPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF 316
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316

   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  (0, 0)

(no "SCOP Domain" information available for 3EHZ)

(-) CATH Domains  (2, 10)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EHZ)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (GLIC_GLOVI | Q7NDN8)
molecular function
    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: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:0005272    sodium channel activity    Enables the facilitated diffusion of a sodium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
biological process
    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: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:0035725    sodium ion transmembrane transport    A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006814    sodium ion transport    The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLIC_GLOVI | Q7NDN82xq3 2xq4 2xq5 2xq6 2xq7 2xq8 2xq9 2xqa 3eam 3ei0 3igq 3lsv 3p4w 3p50 3tls 3tlt 3tlu 3tlv 3tlw 3uu3 3uu4 3uu5 3uu6 3uu8 3uub 4f8h 4hfb 4hfc 4hfd 4hfe 4hfh 4hfi 4il4 4il9 4ila 4ilb 4ilc 4ire 4lmj 4lmk 4lml 4npp 4npq 4qh1 4qh4 4qh5 4x5t 4yeu 4zzb 4zzc 5hcj 5hcm 5heg 5heh 5iux 5j0z 5l47 5l4e 5l4h

(-) Related Entries Specified in the PDB File

3ei0 STRUCTURE OF THE E221A MUTANT OF THE GLOEBACTER VIOLACEUS PENTAMERIC LIGAND GATED ION CHANNNEL (GLIC)