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(-) Description

Title :  CRYSTAL STRUCTURE OF APLYSIA ACHBP IN COMPLEX WITH 4-0H-DMXBA
 
Authors :  G. Sulzenbacher, R. Hibbs, J. Shi, T. Talley, S. Conrod, W. Kem, P. Taylor, P. Marchot, Y. Bourne
Date :  07 Jul 09  (Deposition) - 01 Sep 09  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Receptor, 4-0H-Dmxba, Acetylcholine Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Hibbs, G. Sulzenbacher, J. Shi, T. Talley, S. Conrod, W. Kem, W. Kem, P. Taylor, P. Marchot, Y. Bourne
Structural Determinants For Interaction Of Partial Agonists With Acetylcholine Binding Protein And Neuronal Alpha7 Nicotinic Acetylcholine Receptor.
Embo J. V. 28 3040 2009
PubMed-ID: 19696737  |  Reference-DOI: 10.1038/EMBOJ.2009.227

(-) Compounds

Molecule 1 - SOLUBLE ACETYLCHOLINE RECEPTOR
    Cell: SENSORY CELL
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: RESIDUES 18-236
    Organism Common: CALIFORNIA SEA HARE
    Organism Scientific: APLYSIA CALIFORNICA
    Organism Taxid: 6500
    Synonym: ACETYLCHOLINE BINDING PROTEIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZY55Ligand/Ion4-[(E)-5,6-DIHYDRO-2,3'-BIPYRIDIN-3(4H)-YLIDENEMETHYL]-3-METHOXYPHENOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:93 , TRP A:147 , THR E:36 , TYR E:55 , ILE E:118 , ASP E:164 , SER E:166 , SER E:167 , HOH E:2032BINDING SITE FOR RESIDUE ZY5 A 301
02AC2SOFTWAREASN A:74 , NAG A:402BINDING SITE FOR RESIDUE NAG A 401
03AC3SOFTWARENAG A:401 , BMA A:403 , MAN A:405 , HOH A:2179BINDING SITE FOR RESIDUE NAG A 402
04AC4SOFTWARENAG A:402 , MAN A:404 , MAN A:405 , HOH A:2178 , ASN C:70BINDING SITE FOR RESIDUE BMA A 403
05AC5SOFTWAREBMA A:403 , HOH A:2179 , ARG C:8 , GLU C:71 , GLU C:135BINDING SITE FOR RESIDUE MAN A 404
06AC6SOFTWARENAG A:402 , BMA A:403BINDING SITE FOR RESIDUE MAN A 405
07AC7SOFTWARETHR A:36 , ILE A:118 , ASP A:164 , SER A:166 , SER A:167 , HOH A:2053 , HOH A:2125 , TYR B:93 , TRP B:147BINDING SITE FOR RESIDUE ZY5 B 301
08AC8SOFTWAREASN B:74BINDING SITE FOR RESIDUE NAG B 401
09AC9SOFTWARETHR B:36 , ILE B:118 , ASP B:164 , SER B:166 , SER B:167 , HOH B:2100 , TYR C:93 , TRP C:147 , TYR C:188 , CYS C:190 , TYR C:195BINDING SITE FOR RESIDUE ZY5 C 301
10BC1SOFTWARETHR C:36 , TYR C:55 , GLN C:57 , ILE C:118 , ASP C:164 , SER C:166 , SER C:167 , HOH C:2025 , HOH C:2091 , TYR D:93 , TRP D:147BINDING SITE FOR RESIDUE ZY5 D 301
11BC2SOFTWARETHR D:36 , GLN D:57 , ILE D:118 , ASP D:164 , SER D:166 , SER D:167 , HOH D:2090 , TYR E:93 , TRP E:147 , TYR E:195BINDING SITE FOR RESIDUE ZY5 E 301

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:127 -A:140
2A:190 -A:191
3B:127 -B:140
4B:190 -B:191
5C:127 -C:140
6C:190 -C:191
7D:127 -D:140
8E:127 -E:140
9E:190 -E:191

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WN9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WN9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WN9)

(-) Exons   (0, 0)

(no "Exon" information available for 2WN9)

(-) 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:209
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:209
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
         Q8WSF8_APLCA    17 AHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 225
               SCOP domains d2wn9a_ A: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.............eeee...eeeeeeeee....eeeeeee..eee.hhhhh.hhhhh....eeeee.hhh..............ee....eeeee....eee..eeeeeee............eeeeee.........eeee................eeeeeeeeeeeee........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wn9 A   0 LHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 208
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199         


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:211
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
         Q8WSF8_APLCA    14 VGQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d2wn9b_ B: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.............eeee...eeeeeeeee....eeeeeee..eee.hhhhh.hhhhh....eeeee.hhh..............ee....eeeee....eee..eeeeeee............eeeeee.........eeee................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wn9 B  -3 DDKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 207
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206 


Chain C from PDB  Type:PROTEIN  Length:214
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:214
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221    
         Q8WSF8_APLCA    12 ACVGQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 225
               SCOP domains d2wn9c_ C: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.............eeee...eeeeeeeee....eeeeeee..eee.hhhhh.hhhhh....eeeee.hhh..............ee....eeeee....eee..eeeeeee............eeeeee.........eeee................eeeeeeeeeeeee........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wn9 C  -5 DDDDKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 208
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204    


Chain D from PDB  Type:PROTEIN  Length:205
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:211
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224 
         Q8WSF8_APLCA    15 GQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 225
               SCOP domains d2wn9d_ D: automated   matches                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..--.........eeee...eeeeeeeee....eeeeeee..eee.hhhhh.hhhhh....eeeee.hhh..............ee....eeeee....eee..eeeeeee............eeeeee.........eeee................eeeeeeeeeeeee.----...eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wn9 D  -2 DKLHSQANLMRLKSDLFNRS--YPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQH----PEPYIDVNLVVKFRERR 208
                                     7        17  |     27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    |  197       207 
                                              17 20                                                                                                                                                                    187  192                


Chain E from PDB  Type:PROTEIN  Length:214
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:216
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218      
         Q8WSF8_APLCA     9 LLVACVGQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d2wn9e_ E: automated match  es                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------Neur_chan_LB  D-2wn9E01 E:6-207                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) --------------Neur_chan_LB  D-2wn9E02 E:6-207                                                                                                                                                                            Pfam domains (2)
           Pfam domains (3) --------------Neur_chan_LB  D-2wn9E03 E:6-207                                                                                                                                                                            Pfam domains (3)
           Pfam domains (4) --------------Neur_chan_LB  D-2wn9E04 E:6-207                                                                                                                                                                            Pfam domains (4)
           Pfam domains (5) --------------Neur_chan_LB  D-2wn9E05 E:6-207                                                                                                                                                                            Pfam domains (5)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..--.........eeee...eeeeeeeee....eeeeeee..eee.hhhhh.hhhhh....eeeee.hhh..............ee....eeeee....eee..eeeeeee............eeeeee.........eeee................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wn9 E  -8 DYKDDDDKLHSQANLMRLKSDLFNRS--YPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 207
                                     1        11     |  21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
                                                    17 20
   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, 5)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WN9)

(-) Pfam Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Neur_chan_LBD] (30)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (Q8WSF8_APLCA | Q8WSF8)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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: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.

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  2wn9
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 Related Entries

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

UniProtKB/TrEMBL
        Q8WSF8_APLCA | Q8WSF8: 2br7 2br8 2byn 2byp 2byq 2byr 2bys 2c9t 2pgz 2ph9 2uz6 2w8f 2w8g 2wnc 2wnj 2wnl 2wzy 2x00 2xnt 2xnu 2xnv 2xys 2xyt 2xz5 2xz6 2y54 2y56 2y57 2y58 2y7y 2ymd 2yme 3c79 3c84 3gua 3peo 3pmz 3sh1 3sio 3t4m 4aft 4bfq 4bqt 4dbm 4ez1 4frr 4wv9 4xhe 4xk9 4zjs 4zk4 5ain 5brx 5bw2 5co5 5jme 5ke4 5kzu 5lxb 5syo 5tvc

(-) Related Entries Specified in the PDB File

2br7 CRYSTAL STRUCTURE OF ACETYLCHOLINE-BINDING PROTEIN (ACHBP) FROM APLYSIA CALIFORNICA IN COMPLEX WITH HEPES
2br8 CRYSTAL STRUCTURE OF ACETYLCHOLINE-BINDING PROTEIN (ACHBP) FROM APLYSIA CALIFORNICA IN COMPLEX WITH AN ALPHA-CONOTOXIN PNIA VARIANT
2byn CRYSTAL STRUCTURE OF APO ACHBP FROM APLYSIA CALIFORNICA
2byp CRYSTAL STRUCTURE OF APLYSIA CALIFORNICA ACHBP IN COMPLEX WITH ALPHA-CONOTOXIN IMI
2byq CRYSTAL STRUCTURE OF APLYSIA CALIFORNICA ACHBP IN COMPLEX WITH EPIBATIDINE
2byr CRYSTAL STRUCTURE OF ACHBP FROM APLYSIA CALIFORNICA IN COMPLEX WITH METHYLLYCACONITINE
2bys CRYSTAL STRUCTURE OF ACHBP FROM APLYSIA CALIFORNICA IN COMPLEX WITH LOBELINE
2c9t CRYSTAL STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) FROM APLYSIA CALIFORNICA IN COMPLEX WITH ALPHA-CONOTOXIN IMI
2uz6 ACHBP-TARGETED A-CONOTOXIN CORRELATES DISTINCT BINDING ORIENTATIONS WITH NACHR SUBTYPE SELECTIVITY.
2w8e APLYSIA CALIFORNICA ACHBP IN APO STATE
2w8f APLYSIA CALIFORNICA ACHBP BOUND TO IN SILICO COMPOUND 31
2w8g APLYSIA CALIFORNICA ACHBP BOUND TO IN SILICO COMPOUND 35