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(-) Description

Title :  X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP)
 
Authors :  K. Brejc, W. J. Van Dijk, R. Klaassen, M. Schuurmans, J. Van Der Oost, A. B. Smit, T. K. Sixma
Date :  18 Mar 01  (Deposition) - 16 May 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (1x)
Biol. Unit 2:  A,B,C,D,E  (2x)
Keywords :  Pentamer, Igg Fold, Ligand Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Brejc, W. J. Van Dijk, R. V. Klaassen, M. Schuurmans, J. Van Der Oost, A. B. Smit, T. K. Sixma
Crystal Structure Of An Ach-Binding Protein Reveals The Ligand-Binding Domain Of Nicotinic Receptors.
Nature V. 411 269 2001
PubMed-ID: 11357122  |  Reference-DOI: 10.1038/35077011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACETYLCHOLINE BINDING PROTEIN
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9
    Expression System Strain: GS 115
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: GREAT POND SNAIL
    Organism Scientific: LYMNAEA STAGNALIS
    Organism Taxid: 6523
    Synonym: ACHBP

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): ABCDE
Biological Unit 2 (2x): ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2EPE5Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EPE5Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EPE10Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:161 , ASP A:175 , VAL A:176BINDING SITE FOR RESIDUE CA A 301
02AC2SOFTWAREASP B:161 , ASP B:175 , VAL B:176BINDING SITE FOR RESIDUE CA B 302
03AC3SOFTWAREASP C:161 , VAL C:176BINDING SITE FOR RESIDUE CA C 303
04AC4SOFTWAREASP D:161 , VAL D:176BINDING SITE FOR RESIDUE CA D 304
05AC5SOFTWAREASP E:161 , ASP E:175 , VAL E:176BINDING SITE FOR RESIDUE CA E 305
06AC6SOFTWAREASP A:2 , ASP A:5 , ASP D:2 , ASP D:5BINDING SITE FOR RESIDUE CA E 306
07AC7SOFTWAREASP B:2 , ASP B:5 , ASP C:2 , ASP C:5BINDING SITE FOR RESIDUE CA A 307
08AC8SOFTWAREASP E:2 , ASP E:5BINDING SITE FOR RESIDUE CA E 310
09AC9SOFTWARETRP A:143 , TYR A:185 , TRP B:53 , LEU B:112 , MET B:114BINDING SITE FOR RESIDUE EPE A 1050
10BC1SOFTWARETYR B:89 , TRP B:143 , THR B:144 , TYR B:185 , TRP C:53BINDING SITE FOR RESIDUE EPE B 1051
11BC2SOFTWARETRP C:143 , TYR C:185 , TYR C:192 , TRP D:53 , ARG D:104 , MET D:114BINDING SITE FOR RESIDUE EPE C 1052
12BC3SOFTWARETYR D:89 , SER D:142 , TRP D:143 , THR D:144 , TYR D:185 , TYR D:192 , ARG E:104 , LEU E:112 , MET E:114BINDING SITE FOR RESIDUE EPE D 1053
13BC4SOFTWAREMET A:114 , TYR E:89 , TRP E:143 , TYR E:185 , CYS E:188 , TYR E:192BINDING SITE FOR RESIDUE EPE E 1054

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:123 -A:136
2A:187 -A:188
3B:123 -B:136
4B:187 -B:188
5C:123 -C:136
6C:187 -C:188
7D:123 -D:136
8D:187 -D:188
9E:123 -E:136
10E:187 -E:188

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I9B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I9B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I9B)

(-) Exons   (0, 0)

(no "Exon" information available for 1I9B)

(-) Sequences/Alignments

Asymmetric 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:205
 aligned with ACHP_LYMST | P58154 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:205
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
           ACHP_LYMST    20 LDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKG 224
               SCOP domains d1i9ba_ A: Acetylcholine binding protein (ACHBP)                                                                                                                                                              SCOP domains
               CATH domains 1i9bA00 A:1-205  [code=2.70.170.10, no name defined]                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh........eeeee.hhh....eee.......ee....eeeee...eeee..eeeeeee...........eeeeeeeee.......eeee.................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9b A   1 FDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKG 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with ACHP_LYMST | P58154 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:205
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
           ACHP_LYMST    20 LDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKG 224
               SCOP domains d1i9bb_ B: Acetylcholine binding protein (ACHBP)                                                                                                                                                              SCOP domains
               CATH domains 1i9bB00 B:1-205  [code=2.70.170.10, no name defined]                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh........eeeee.hhh....eee.......ee....eeeee...eeee..eeeeeee...........eeeeeeeee.......eeee.................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9b B   1 FDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKG 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     


Chain C from PDB  Type:PROTEIN  Length:205
 aligned with ACHP_LYMST | P58154 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:205
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
           ACHP_LYMST    20 LDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKG 224
               SCOP domains d1i9bc_ C: Acetylcholine binding protein (ACHBP)                                                                                                                                                              SCOP domains
               CATH domains 1i9bC00 C:1-205  [code=2.70.170.10, no name defined]                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh........eeeee.hhh....eee.......ee....eeeee...eeee..eeeeeee...........eeeeeeeee.......eeee.................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9b C   1 FDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKG 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     


Chain D from PDB  Type:PROTEIN  Length:205
 aligned with ACHP_LYMST | P58154 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:205
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
           ACHP_LYMST    20 LDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKG 224
               SCOP domains d1i9bd_ D: Acetylcholine binding protein (ACHBP)                                                                                                                                                              SCOP domains
               CATH domains 1i9bD00 D:1-205  [code=2.70.170.10, no name defined]                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh........eeeee.hhh....eee.......ee....eeeee...eeee..eeeeeee...........eeeeeeeee.......eeee.................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9b D   1 FDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKG 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     


Chain E from PDB  Type:PROTEIN  Length:205
 aligned with ACHP_LYMST | P58154 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:205
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
           ACHP_LYMST    20 LDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKG 224
               SCOP domains d1i9be_ E: Acetylcholine binding protein (ACHBP)                                                                                                                                                              SCOP domains
               CATH domains 1i9bE00 E:1-205  [code=2.70.170.10, no name defined]                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh........eeeee.hhh....eee.......ee....eeeee...eeee..eeeeeee...........eeeeeeeee.......eeee.................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9b E   1 FDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKG 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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 5)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I9B)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (ACHP_LYMST | P58154)
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.
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:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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  1i9b
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  ACHP_LYMST | P58154
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 Related Entries

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

UniProtKB/Swiss-Prot
        ACHP_LYMST | P58154: 1uv6 1uw6 1ux2 1yi5 2zju 2zjv 3u8j 3u8k 3u8l 3u8m 3u8n 3wip 3wth 3wti 3wtj 3wtk 3wtl 3wtm 3wtn 3wto 3zdg 3zdh 4alx 4hqp 4nzb 4qaa 4qab 4qac 4um1 4um3 4zjt 4zk1 4zr6 4zru 5afh 5afj 5afk 5afl 5afm 5afn 5bp0 5j5f 5j5g 5j5h 5j5i 5t90

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1I9B)