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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  APLYSIA CALIFORNICA ACHBP IN APO STATE
 
Authors :  C. Ulens, A. Akdemir, A. Jongejan, R. Van Elk, S. Bertrand, A. Perrakis A. B. Smit, T. K. Sixma, D. Bertrand, I. J. De Esch
Date :  02 Feb 11  (Deposition) - 23 Mar 11  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Receptor, Secreted, Amidation, Conotoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Ulens, A. Akdemir, A. Jongejan, R. Van Elk, S. Bertrand, A. Perrakis, R. Leurs, A. B. Smit, T. K. Sixma, D. Bertrand, I. J. De Esc
Use Of Acetylcholine Binding Protein In The Search For Novel Alpha7 Nicotinic Receptor Ligands. In Silico Docking, Pharmacological Screening, And X-Ray Analysis.
J. Med. Chem. V. 52 2372 2009
PubMed-ID: 19331415  |  Reference-DOI: 10.1021/JM801400G

(-) Compounds

Molecule 1 - SOLUBLE ACETYLCHOLINE RECEPTOR
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMY WORM
    Expression System Plasmid: PFASTBAC
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: RESIDUES 20-236
    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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2Y7Y)

(-) Sites  (0, 0)

(no "Site" information available for 2Y7Y)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:125 -A:138
2B:125 -B:138
3C:125 -C:138
4D:125 -D:138
5E:125 -E:138
6E:188 -E:189

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y7Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y7Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y7Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y7Y)

(-) 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:203
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:205
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
         Q8WSF8_APLCA    20 QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d2y7ya_ A: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.hhhhh....eeeee.hhh....eee.......ee....eeeee.eeeeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee...--...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7y A   1 QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKVDSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGVTCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYS--PEPYIDVNLVVKFRER 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      |190       200     
                                                                                                                                                                                                                    187  |               
                                                                                                                                                                                                                       190               


Chain B from PDB  Type:PROTEIN  Length:201
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:205
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
         Q8WSF8_APLCA    20 QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d2y7yb_ B: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.hhhhhh...eeeee.hhh....eee.......ee....eeeee.eeeeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee.----...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7y B   1 QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKVDSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGVTCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQH----PEPYIDVNLVVKFRER 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |  190       200     
                                                                                                                                                                                                                  185  190               


Chain C from PDB  Type:PROTEIN  Length:201
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:205
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
         Q8WSF8_APLCA    20 QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d2y7yc_ C: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.hhhhh....eeeee.hhh....eee.......ee....eeeee.eeeeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee.----...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7y C   1 QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKVDSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGVTCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQH----PEPYIDVNLVVKFRER 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |  190       200     
                                                                                                                                                                                                                  185  190               


Chain D from PDB  Type:PROTEIN  Length:200
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:205
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
         Q8WSF8_APLCA    20 QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d2y7yd_ D: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.hhhhhh...eeeee.hhh....eee.......ee....eeeee.eeeeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee.-----..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7y D   1 QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKVDSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGVTCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQH-----EPYIDVNLVVKFRER 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    |    -|      200     
                                                                                                                                                                                                                  185   191              


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

    Alignment length:205
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
         Q8WSF8_APLCA    20 QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d2y7ye_ E: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Neur_chan_LBD-2y7yE01 E:4-205                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) ---Neur_chan_LBD-2y7yE02 E:4-205                                                                                                                                                                              Pfam domains (2)
           Pfam domains (3) ---Neur_chan_LBD-2y7yE03 E:4-205                                                                                                                                                                              Pfam domains (3)
           Pfam domains (4) ---Neur_chan_LBD-2y7yE04 E:4-205                                                                                                                                                                              Pfam domains (4)
           Pfam domains (5) ---Neur_chan_LBD-2y7yE05 E:4-205                                                                                                                                                                              Pfam domains (5)
         Sec.struct. author hhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.hhhhhh...eeeee.hhh....eee.......ee....eeeee.eeeeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7y E   1 QANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKVDSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGVTCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 2Y7Y)

(-) 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 across a membrane.
    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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  2y7y
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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 2wn9 2wnc 2wnj 2wnl 2wzy 2x00 2xnt 2xnu 2xnv 2xys 2xyt 2xz5 2xz6 2y54 2y56 2y57 2y58 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.
2w8f APLYSIA CALIFORNICA ACHBP BOUND TO IN SILICO COMPOUND 31
2w8g APLYSIA CALIFORNICA ACHBP BOUND TO IN SILICO COMPOUND 35
2wn9 CRYSTAL STRUCTURE OF APLYSIA ACHBP IN COMPLEX WITH 4- 0H-DMXBA
2wnc CRYSTAL STRUCTURE OF APLYSIA ACHBP IN COMPLEX WITH TROPISETRON
2wnj CRYSTAL STRUCTURE OF APLYSIA ACHBP IN COMPLEX WITH DMXBA
2wnl CRYSTAL STRUCTURE OF APLYSIA ACHBP IN COMPLEX WITH ANABASEINE
2wzy CRYSTAL STRUCTURE OF A-ACHBP IN COMPLEX WITH 13- DESMETHYL SPIROLIDE C
2x00 CRYSTAL STRUCTURE OF A-ACHBP IN COMPLEX WITH GYMNODIMINE A
2xnt ACETYLCHOLINE BINDING PROTEIN (ACHBP) AS TEMPLATE FOR HIERARCHICAL IN SILICO SCREENING PROCEDURES TO IDENTIFY STRUCTURALLY NOVEL LIGANDS FOR THE NICOTINIC RECEPTORS
2xnu ACETYLCHOLINE BINDING PROTEIN (ACHBP) AS TEMPLATE FOR HIERARCHICAL IN SILICO SCREENING PROCEDURES TO IDENTIFY STRUCTURALLY NOVEL LIGANDS FOR THE NICOTINIC RECEPTORS
2xnv ACETYLCHOLINE BINDING PROTEIN (ACHBP) AS TEMPLATE FOR HIERARCHICAL IN SILICO SCREENING PROCEDURES TO IDENTIFY STRUCTURALLY NOVEL LIGANDS FOR THE NICOTINIC RECEPTORS
2xys CRYSTAL STRUCTURE OF APLYSIA CALIFORNICA ACHBP IN COMPLEX WITH STRYCHNINE
2xyt CRYSTAL STRUCTURE OF APLYSIA CALIFORNICA ACHBP IN COMPLEX WITH D-TUBOCURARINE
2xz5 MMTS-MODIFIED Y53C MUTANT OF APLYSIA ACHBP IN COMPLEX WITH ACETYLCHOLINE
2xz6 MTSET-MODIFIED Y53C MUTANT OF APLYSIA ACHBP
2y54 FRAGMENT GROWING INDUCES CONFORMATIONAL CHANGES IN ACETYLCHOLINE-BINDING PROTEIN: A STRUCTURAL AND THERMODYNAMIC ANALYSIS - (FRAGMENT 1)
2y57 FRAGMENT GROWING INDUCES CONFORMATIONAL CHANGES IN ACETYLCHOLINE-BINDING PROTEIN: A STRUCTURAL AND THERMODYNAMIC ANALYSIS - (COMPOUND 4)
2y58 FRAGMENT GROWING INDUCES CONFORMATIONAL CHANGES IN ACETYLCHOLINE-BINDING PROTEIN: A STRUCTURAL AND THERMODYNAMIC ANALYSIS - (COMPOUND 6)