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- PDB-3wtn: Crystal Structure of Lymnaea stagnalis Acetylcholine Binding Prot... -

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Basic information

Entry
Database: PDB / ID: 3wtn
TitleCrystal Structure of Lymnaea stagnalis Acetylcholine Binding Protein Complexed with Desnitro-imidacloprid
ComponentsAcetylcholine-binding protein
KeywordsSIGNALING PROTEIN / neonicotinoids / nicotinic acetylcholine receptor / imidacloprid / acetylcholine binding
Function / homology
Function and homology information


synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / synapse / membrane
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Ig-like domain profile. / Immunoglobulin-like domain / Mainly Beta
Similarity search - Domain/homology
: / Chem-N2Y / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsOkajima, T. / Ihara, M. / Yamashita, A. / Oda, T. / Matsuda, K.
CitationJournal: Mol.Pharmacol. / Year: 2014
Title: Studies on an acetylcholine binding protein identify a basic residue in loop G on the beta 1 strand as a new structural determinant of neonicotinoid actions
Authors: Ihara, M. / Okajima, T. / Yamashita, A. / Oda, T. / Asano, T. / Matsui, M. / Sattelle, D.B. / Matsuda, K.
History
DepositionApr 11, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
F: Acetylcholine-binding protein
G: Acetylcholine-binding protein
H: Acetylcholine-binding protein
I: Acetylcholine-binding protein
J: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,44176
Polymers242,21810
Non-polymers8,22366
Water24,0681336
1
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,14347
Polymers121,1095
Non-polymers5,03442
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Acetylcholine-binding protein
G: Acetylcholine-binding protein
H: Acetylcholine-binding protein
I: Acetylcholine-binding protein
J: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,29829
Polymers121,1095
Non-polymers3,18924
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,33210
Polymers24,2221
Non-polymers1,1109
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,24210
Polymers24,2221
Non-polymers1,0219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,24210
Polymers24,2221
Non-polymers1,0219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2199
Polymers24,2221
Non-polymers9988
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
E: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1078
Polymers24,2221
Non-polymers8857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
F: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8826
Polymers24,2221
Non-polymers6605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
G: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9957
Polymers24,2221
Non-polymers7736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
H: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6574
Polymers24,2221
Non-polymers4353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
I: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1078
Polymers24,2221
Non-polymers8857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
J: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6574
Polymers24,2221
Non-polymers4353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.006, 118.401, 243.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acetylcholine-binding protein / ACh-binding protein / AchBP


Mass: 24221.811 Da / Num. of mol.: 10 / Fragment: UNP residues 21-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Plasmid: pPICZ B / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P58154
#2: Chemical
ChemComp-N2Y / (2Z)-1-[(6-chloropyridin-3-yl)methyl]imidazolidin-2-imine


Mass: 210.663 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C9H11ClN4
#3: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1336 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT BEFORE CRYSTALLIZATION, THE N-GLUCOSIDE GROUPS WERE REMOVED BY PEPTIDE-N- ...AUTHORS STATE THAT BEFORE CRYSTALLIZATION, THE N-GLUCOSIDE GROUPS WERE REMOVED BY PEPTIDE-N-GLYCOSIDASE F. THE CONFLICT IS DUE TO POST-TRANSLATIONAL MODIFICATION AND SAMPLE PREPARATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 1.5M Na acetate, 0.05M CdSO4, 0.1M HEPES-Na (pH 7.5), 0.5mM Desnitro-imidacloprid, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 13, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. all: 137631 / Num. obs: 131277 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.09→2.18 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.8 / Num. unique all: 12230 / % possible all: 93.7

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Processing

Software
NameVersionClassification
BBSdata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZJU

2zju


Resolution: 2.09→47.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2790612.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 6567 5 %RANDOM
Rwork0.213 ---
all0.216 131114 --
obs0.213 131114 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.3895 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.02 Å20 Å20 Å2
2---7.31 Å20 Å2
3----0.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.09→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16520 0 196 1336 18052
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.09→2.22 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 1051 5.1 %
Rwork0.27 19559 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5dni.pardni.top

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