2ZJV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LYMNAEA STAGNALIS ACETYLCHOLINE BINDING PROTEIN (LS-ACHBP) COMPLEXED WITH CLOTHIANIDIN

Authors :   T. Okajima, M. Ihara, A. Yamashita, T. Oda, T. Morimoto, K. Matsuda

Date :   10 Mar 08 (Deposition) - 08 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B,C,D,E

Keywords :   Acetylcholine Binding Protein, Neonicotinoids, Nicotinic Acetylcholine Receptor, Clothianidin, Cell Junction, Glycoprotein, Immunoglobulin Domain, Secreted, Synapse, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Ihara, T. Okajima, A. Yamashita, T. Oda, K. Hirata, H. Nishiwaki, T. Morimoto, M. Akamatsu, Y. Ashikawa, S. Kuroda, R. Mega, S. Kuramitsu, D. B. Sattelle, K. Matsuda
Crystal Structures Of Lymnaea Stagnalis Achbp In Complex With Neonicotinoid Insecticides Imidacloprid And Clothianidin
Invert. Neurosci. V. 8 71 2008
PubMed-ID: 18338186 | Reference-DOI: 10.1007/S10158-008-0069-3
(for further references see the PDB file header)

Molecule 1 - ACETYLCHOLINE-BINDING PROTEIN
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Common	:	FUNGI
	Expression System Plasmid	:	PPICZB
	Expression System Strain	:	X-33
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 16-229
	Mutation	:	YES
	Organism Common	:	GREAT POND SNAIL
	Organism Scientific	:	LYMNAEA STAGNALIS
	Synonym	:	ACH-BINDING PROTEIN, ACHBP

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	CT4	5	Ligand/Ion	1-[(2-CHLORO-1,3-THIAZOL-5-YL)METHYL]-3-METHYL-2-NITROGUANIDINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:143 , TYR A:185 , CYS A:187 , TYR A:192 , TRP B:53 , LEU B:102 , ARG B:104 , LEU B:112 , MET B:114	BINDING SITE FOR RESIDUE CT4 A 301
2	AC2	SOFTWARE	TYR B:89 , TRP B:143 , TYR B:185 , CYS B:187 , TYR B:192 , TRP C:53 , ARG C:104 , LEU C:112 , MET C:114	BINDING SITE FOR RESIDUE CT4 B 301
3	AC3	SOFTWARE	TRP C:143 , THR C:144 , TYR C:185 , CYS C:187 , TYR C:192 , TRP D:53 , ARG D:104 , LEU D:112 , TYR D:113 , MET D:114	BINDING SITE FOR RESIDUE CT4 C 301
4	AC4	SOFTWARE	TRP D:143 , TYR D:185 , CYS D:187 , TRP E:53 , GLN E:55 , ARG E:104 , LEU E:112 , MET E:114	BINDING SITE FOR RESIDUE CT4 D 301
5	AC5	SOFTWARE	TRP A:53 , LEU A:102 , ARG A:104 , LEU A:112 , MET A:114 , TYR E:89 , TRP E:143 , THR E:144 , TYR E:185 , CYS E:187 , TYR E:192	BINDING SITE FOR RESIDUE CT4 E 301

Asymmetric/Biological Unit

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

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

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

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

(no "Exon" information available for 2ZJV)

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:208
 aligned with ACHP_LYMST | P58154 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:208
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
           ACHP_LYMST    19 SLDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRS 226
               SCOP domains d2zjva_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2zjvA00 A:0-207  [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.......eeeee................eeeeeeeeeeeeee......eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zjv A   0 AADRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWDSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRS 207
                                     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:208
 aligned with ACHP_LYMST | P58154 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:208
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219        
           ACHP_LYMST    20 LDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRSE 227
               SCOP domains d2zjvb_ B: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2zjvB00 B:1-208  [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.......eeeee................eeeeeeeeeeeeee......eeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zjv B   1 ADRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWDSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRSE 208
                                    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:207
 aligned with ACHP_LYMST | P58154 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:207
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       
           ACHP_LYMST    20 LDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRS 226
               SCOP domains d2zjvc_ C: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 2zjvC00 C:1-207  [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.................eeeeeeeeeeeee........eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zjv C   1 ADRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWDSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRS 207
                                    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:208
 aligned with ACHP_LYMST | P58154 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:208
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
           ACHP_LYMST    19 SLDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRS 226
               SCOP domains d2zjvd_ D: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2zjvD00 D:0-207  [code=2.70.170.10, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh............eeeeeeeeeeeeeeee....eeeeeeeeeeeee......hhhhh..eeeee.hhh....eee.......ee....eeeee...eeee..eeeeeee...........eeeeeeeee.......eeeee................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zjv D   0 AADRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWDSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRS 207
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199

Chain E from PDB  Type:PROTEIN  Length:208
 aligned with ACHP_LYMST | P58154 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:208
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
           ACHP_LYMST    19 SLDRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRS 226
               SCOP domains d2zjve_ E: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2zjvE00 E:0-207  [code=2.70.170.10, no name defined]                                                                                                                                                             CATH domains
           Pfam domains (1) ---Neur_chan_LBD-2zjvE01 E:3-205                                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) ---Neur_chan_LBD-2zjvE02 E:3-205                                                                                                                                                                              -- Pfam domains (2)
           Pfam domains (3) ---Neur_chan_LBD-2zjvE03 E:3-205                                                                                                                                                                              -- Pfam domains (3)
           Pfam domains (4) ---Neur_chan_LBD-2zjvE04 E:3-205                                                                                                                                                                              -- Pfam domains (4)
           Pfam domains (5) ---Neur_chan_LBD-2zjvE05 E:3-205                                                                                                                                                                              -- Pfam domains (5)
         Sec.struct. author ..hhhhhhhhhhhhh............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh........eeeee.hhh....eee.......ee....eeeee...eeee..eeeeeee...........eeeeeeeee.......eeee.................eeeeeeeeeeeeee......eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zjv E   0 AADRADILYNIRQTSRPDVIPTQRDRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWDSSHSPDQVSVPISSLWVPDLAAYNAISKPEVLTPQLARVVSDGEVLYMPSIRQRFSCDVSGVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYSCCPEAYEDVEVSLNFRKKGRS 207
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Nicotinic receptor ligand binding domain-like (58)

Superfamily: Nicotinic receptor ligand binding domain-like (58)

Family: Nicotinic receptor ligand binding domain-like (18)

Protein domain: automated matches (11)

Great pond snail (Lymnaea stagnalis) [TaxId: 6523] (9)

1a	d2zjva_	A:
1b	d2zjvb_	B:
1c	d2zjvc_	C:
1d	d2zjvd_	D:
1e	d2zjve_	E:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Distorted Sandwich (506)

Topology: Acetylcholine Binding Protein; Chain: A, (12)

Homologous Superfamily: [code=2.70.170.10, no name defined] (12)

Great pond snail (Lymnaea stagnalis) (6)

1a	2zjvC00	C:1-207
1b	2zjvA00	A:0-207
1c	2zjvB00	B:1-208
1d	2zjvD00	D:0-207
1e	2zjvE00	E:0-207

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Neur_chan_LBD] (30)

Family: Neur_chan_LBD (30)

Lymnaea stagnalis (Great pond snail) (5)

1a	Neur_chan_LBD-2zjvE01	E:3-205
1b	Neur_chan_LBD-2zjvE02	E:3-205
1c	Neur_chan_LBD-2zjvE03	E:3-205
1d	Neur_chan_LBD-2zjvE04	E:3-205
1e	Neur_chan_LBD-2zjvE05	E:3-205

Asymmetric/Biological 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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	2zjv
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (10, 10)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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SCOP Domains (1, 5)

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