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(-) Description

Title :  THE PENTAMERIC LIGAND-GATED ION CHANNEL GLIC A237F IN COMPLEX WITH RUBIDIUM
 
Authors :  L. Sauguet, P. J. Corringer, M. Delarue
Date :  29 Dec 12  (Deposition) - 20 Feb 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Pentameric Ligand-Gated Ion Channel, Ion Channel, Membrane, Membrane Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Sauguet, F. Poitevin, S. Murail, C. Van Renterghem, G. Moraga-Cid L. Malherbe, A. W. Thompson, P. Koehl, P. J. Corringer, M. Baaden, M. Delarue
Structural Basis For Ion Permeation Mechanism In Pentameric Ligand-Gated Ion Channels.
Embo J. V. 32 728 2013
PubMed-ID: 23403925  |  Reference-DOI: 10.1038/EMBOJ.2013.17

(-) Compounds

Molecule 1 - PROTON-GATED ION CHANNEL
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 C43
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 44-358
    Gene: GLVI, GLR4197
    Mutation: YES
    Organism Scientific: GLOEOBACTER VIOLACEUS
    Organism Taxid: 251221
    Strain: PCC 7421
    Synonym: GLIC, LIGAND-GATED ION CHANNEL, LGIC

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 48)

Asymmetric/Biological Unit (7, 48)
No.NameCountTypeFull Name
1ACT10Ligand/IonACETATE ION
2CL5Ligand/IonCHLORIDE ION
3LMT6Ligand/IonDODECYL-BETA-D-MALTOSIDE
4NA6Ligand/IonSODIUM ION
5PLC10Ligand/IonDIUNDECYL PHOSPHATIDYL CHOLINE
6RB1Ligand/IonRUBIDIUM ION
7UNL10Ligand/IonUNKNOWN LIGAND

(-) Sites  (35, 35)

Asymmetric Unit (35, 35)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:237 , THR B:244 , LMT B:401BINDING SITE FOR RESIDUE LMT A 401
02AC2SOFTWAREARG A:118 , PHE A:121 , TYR A:194 , TYR A:254 , ASN A:307 , PHE A:315 , PLC A:403BINDING SITE FOR RESIDUE PLC A 402
03AC3SOFTWAREPLC A:402BINDING SITE FOR RESIDUE PLC A 403
04AC4SOFTWAREPHE A:78 , ARG A:85BINDING SITE FOR RESIDUE CL A 406
05AC5SOFTWAREPRO A:68 , ILE A:71 , ILE A:73BINDING SITE FOR RESIDUE NA A 407
06AC6SOFTWAREGLU A:222 , GLU B:222 , GLU C:222 , GLU D:222 , GLU E:222BINDING SITE FOR RESIDUE RB A 408
07AC7SOFTWAREARG A:77 , ILE A:131 , GLU A:181 , PHE E:42 , ARG E:105BINDING SITE FOR RESIDUE ACT A 409
08AC8SOFTWAREILE A:73 , PRO A:74 , ILE A:76 , ARG A:85BINDING SITE FOR RESIDUE ACT A 410
09AC9SOFTWARELMT A:401 , PHE B:237 , PHE C:237BINDING SITE FOR RESIDUE LMT B 401
10BC1SOFTWAREARG B:118 , PHE B:121 , TYR B:194 , TYR B:254 , ASN B:307 , PHE B:315 , PLC B:404BINDING SITE FOR RESIDUE PLC B 403
11BC2SOFTWAREPLC B:403BINDING SITE FOR RESIDUE PLC B 404
12BC3SOFTWAREPHE B:78 , ARG B:85BINDING SITE FOR RESIDUE CL B 407
13BC4SOFTWAREPRO B:68 , ILE B:71 , ILE B:73BINDING SITE FOR RESIDUE NA B 408
14BC5SOFTWAREPHE A:42 , ARG A:105 , ARG B:77 , ILE B:131 , GLU B:181BINDING SITE FOR RESIDUE ACT B 409
15BC6SOFTWAREILE B:73 , PRO B:74 , ILE B:76 , ARG B:85BINDING SITE FOR RESIDUE ACT B 410
16BC7SOFTWAREPHE C:237BINDING SITE FOR RESIDUE LMT C 401
17BC8SOFTWAREARG C:118 , PHE C:121 , TYR C:194 , TYR C:254 , ASN C:307BINDING SITE FOR RESIDUE PLC C 402
18BC9SOFTWAREPHE C:78 , ARG C:85BINDING SITE FOR RESIDUE CL C 406
19CC1SOFTWAREPRO C:68 , ILE C:71BINDING SITE FOR RESIDUE NA C 407
20CC2SOFTWAREPRO C:74 , ILE C:76 , ARG C:85BINDING SITE FOR RESIDUE ACT C 408
21CC3SOFTWAREPHE B:42 , ARG B:105 , ARG C:77 , ILE C:131 , GLU C:181BINDING SITE FOR RESIDUE ACT C 409
22CC4SOFTWARETHR E:244BINDING SITE FOR RESIDUE LMT D 401
23CC5SOFTWAREARG D:118 , PHE D:121 , TYR D:194 , TYR D:254 , ASN D:307 , PHE D:315 , PLC D:403BINDING SITE FOR RESIDUE PLC D 402
24CC6SOFTWAREPLC D:402BINDING SITE FOR RESIDUE PLC D 403
25CC7SOFTWAREPHE D:78 , ARG D:85BINDING SITE FOR RESIDUE CL D 406
26CC8SOFTWAREGLU D:222BINDING SITE FOR RESIDUE NA D 407
27CC9SOFTWAREPRO D:68 , ILE D:71 , TRP D:72 , ILE D:73BINDING SITE FOR RESIDUE NA D 408
28DC1SOFTWAREPRO D:74 , ILE D:76 , ARG D:85BINDING SITE FOR RESIDUE ACT D 409
29DC2SOFTWAREPHE C:42 , ARG C:105 , ARG D:77 , ILE D:131 , GLU D:181BINDING SITE FOR RESIDUE ACT D 410
30DC3SOFTWAREARG E:118 , PHE E:121 , TYR E:194 , TYR E:254 , ASN E:307 , PHE E:315 , PLC E:403BINDING SITE FOR RESIDUE PLC E 402
31DC4SOFTWAREPLC E:402BINDING SITE FOR RESIDUE PLC E 403
32DC5SOFTWAREPHE E:78 , ARG E:85BINDING SITE FOR RESIDUE CL E 406
33DC6SOFTWAREPRO E:68 , ILE E:71BINDING SITE FOR RESIDUE NA E 407
34DC7SOFTWAREPHE D:42 , ARG D:105 , ARG E:77 , ILE E:131 , GLU E:181BINDING SITE FOR RESIDUE ACT E 408
35DC8SOFTWAREPRO E:74 , ILE E:76 , ARG E:85 , TYR E:102BINDING SITE FOR RESIDUE ACT E 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ILB)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Tyr A:119 -Pro A:120
2Tyr B:119 -Pro B:120
3Tyr C:119 -Pro C:120
4Tyr D:119 -Pro D:120
5Tyr E:119 -Pro E:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ILB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ILB)

(-) Exons   (0, 0)

(no "Exon" information available for 4ILB)

(-) 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:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.hhhhhh...ee.hhhhh....eee.......eeeeeeeee....eeeeeeeeeeeee...........eeeeeeeeeee......eeeee.hhhhee........eeeeeeeeeeeeeeeee..eeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ilb A   5 VSPPPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIFFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFF 315
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314 


Chain B from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.hhhhhh...ee.hhhhh....eee.......eeeeeeeee....eeeeeeeeeeeee...........eeeeeeeeeee......eeeee.hhhhee........eeeeeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ilb B   5 VSPPPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIFFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFF 315
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314 


Chain C from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.hhhhhh...ee.hhhhh....eee.......eeeeeeeee....eeeeeeeeeeeee...........eeeeeeeeeee......eeeee.hhhhee........eeeeeeeeeeeeeeeee..eeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ilb C   5 VSPPPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIFFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFF 315
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314 


Chain D from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.hhhhhh...ee.hhhhh....eee.......eeeeeeeee....eeeeeeeeeeeee...........eeeeeeeeeee......eeeee.hhhhee........eeeeeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ilb D   5 VSPPPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIFFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFF 315
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314 


Chain E from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.hhhhhh...ee.hhhhh....eee.......eeeeeeeee....eeeeeeeeeeeee...........eeeeeeeeeee......eeeee.hhhhee........eeeeeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ilb E   5 VSPPPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIFFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFF 315
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314
   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 4ILB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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        GLIC_GLOVI | Q7NDN8: 2xq3 2xq4 2xq5 2xq6 2xq7 2xq8 2xq9 2xqa 3eam 3ehz 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 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

4hfi 4il4 4il9 4ila 4ilc