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- PDB-4alx: Crystal Structure of Ls-AChBP complexed with the potent nAChR ant... -

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Basic information

Entry
Database: PDB / ID: 4alx
TitleCrystal Structure of Ls-AChBP complexed with the potent nAChR antagonist DHbE
ComponentsACETYLCHOLINE BINDING PROTEIN
KeywordsACETYLCHOLINE-BINDING PROTEIN / LYMNAEA STAGNALIS / DIHYDRO-B-ERYTHROIDINE / ANTAGONIST / C-LOOP
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / synaptic cleft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / 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-IZN / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLYMNAEA STAGNALIS (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShahsavar, A. / Kastrup, J.S. / Nielsen, E.O. / Kristensen, J.L. / Gajhede, M. / Balle, T.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of Lymnaea Stagnalis Achbp Complexed with the Potent Nachr Antagonist Dh-Betab-E Suggests a Unique Mode of Antagonism
Authors: Shahsavar, A. / Kastrup, J.S. / Nielsen, E.O. / Kristensen, J.L. / Gajhede, M. / Balle, T.
History
DepositionMar 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)265,20232
Polymers260,87310
Non-polymers4,32922
Water12,394688
1
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)132,83917
Polymers130,4375
Non-polymers2,40312
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14980 Å2
ΔGint-63.8 kcal/mol
Surface area41350 Å2
MethodPISA
2
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)132,36315
Polymers130,4375
Non-polymers1,92610
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14680 Å2
ΔGint-62.7 kcal/mol
Surface area41580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.249, 121.308, 152.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:2 OR RESSEQ 4:21 OR RESSEQ...
211CHAIN B AND (RESSEQ 1:2 OR RESSEQ 4:21 OR RESSEQ...
311CHAIN C AND (RESSEQ 1:2 OR RESSEQ 4:21 OR RESSEQ...
411CHAIN D AND (RESSEQ 1:2 OR RESSEQ 4:21 OR RESSEQ...
511CHAIN E AND (RESSEQ 1:2 OR RESSEQ 4:21 OR RESSEQ...
611CHAIN F AND (RESSEQ 1:2 OR RESSEQ 4:21 OR RESSEQ...
711CHAIN G AND (RESSEQ 1:2 OR RESSEQ 4:21 OR RESSEQ...
811CHAIN H AND (RESSEQ 1:2 OR RESSEQ 4:21 OR RESSEQ...
911CHAIN I AND (RESSEQ 1:2 OR RESSEQ 4:21 OR RESSEQ 26:109 OR RESSEQ 111:154 OR RESSEQ 164:202 )
1011CHAIN J AND (RESSEQ 1:2 OR RESSEQ 4:21 OR RESSEQ...

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.312083, -0.146433, 0.938702), (0.112376, 0.986804, 0.116576), (-0.943385, 0.069106, 0.32442)-7.03101, 5.13143, -39.0114
3given(-0.815055, -0.124515, 0.565845), (0.038218, 0.962953, 0.266949), (-0.578121, 0.239204, -0.780101)-47.2696, 5.31774, -44.8625
4given(-0.803499, 0.048137, -0.593357), (-0.11691, 0.964556, 0.236565), (0.583714, 0.259449, -0.769392)-64.9306, -0.02565, -8.56653
5given(0.31502, 0.119159, -0.941575), (-0.141437, 0.986903, 0.077575), (0.938487, 0.108736, 0.327748)-35.2278, -3.22189, 19.1
6given(-0.704618, 0.121121, -0.699173), (0.087626, -0.962931, -0.255121), (-0.704155, -0.241028, 0.667885)-62.4091, -20.6284, -29.2585
7given(-0.892556, -0.053558, 0.447745), (-0.071072, -0.963804, -0.256965), (0.4453, -0.261177, 0.856443)-50.9771, -25.6471, 8.6772
8given(0.164249, -0.130293, 0.977776), (-0.119539, -0.986562, -0.111383), (0.979149, -0.098588, -0.177617)-11.2945, -25.1392, 9.57055
9given(0.988141, 0.013506, 0.152953), (0.014803, -0.999863, -0.007341), (0.152833, 0.009518, -0.988206)2.11165, -19.3118, -27.6875
10given(0.455383, 0.147228, -0.878038), (0.138744, -0.985918, -0.09336), (-0.879418, -0.079308, -0.469397)-29.5334, -17.0302, -51.4655

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Components

#1: Protein
ACETYLCHOLINE BINDING PROTEIN / ACH-BINDING PROTEIN / ACHBP


Mass: 26087.311 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LYMNAEA STAGNALIS (great pond snail) / Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P58154
#2: Chemical
ChemComp-IZN / (4bS,6S)-6-methoxy-1,4,6,7,9,10,12,13-octahydro-3H,5H-pyrano[4',3':3,4]pyrido[2,1-i]indol-3-one / (2S,13bS)-2-Methoxy-2,3,5,6,8,9,10,13-octahydro-1H,12H-benzo[i]pyrano[3,4-g]indolizin-12-one


Mass: 275.343 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C16H21NO3
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsDIHYDRO-BETA-ERYTHROIDINE (DHBE) BINDS AT THE LIGAND-BINDING POCKET AT THE INTERFACE OF EACH TWO MONOMERS

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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: 2.12 Å3/Da / Density % sol: 43.7 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 25% V/V PEG 400, AND 0.2 M MGCL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.997
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 24, 2011 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.3→20.1 Å / Num. obs: 97154 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.36 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20.158 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 24.8 / Stereochemistry target values: ML
Details: THE F-LOOP PORTION OF THE MOLECULE, RESIDUES 154-160 IN SUBUNITS B AND E AND 155- -160 IN SUBUNITS C, G, H, I, AND J, IS NOT COMPLETELY MODELED DUE TO LACK OF CLEAR ELECTRON DENSITY, ...Details: THE F-LOOP PORTION OF THE MOLECULE, RESIDUES 154-160 IN SUBUNITS B AND E AND 155- -160 IN SUBUNITS C, G, H, I, AND J, IS NOT COMPLETELY MODELED DUE TO LACK OF CLEAR ELECTRON DENSITY, SIGNIFYING A GREATER FLEXIBILITY OF THESE PARTS OF THE PROTEIN.
RfactorNum. reflection% reflection
Rfree0.2504 4863 5 %
Rwork0.2033 --
obs0.2056 97154 98.92 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.442 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3472 Å20 Å20 Å2
2---6.3974 Å20 Å2
3---7.7446 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16170 0 292 688 17150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816901
X-RAY DIFFRACTIONf_angle_d1.12623035
X-RAY DIFFRACTIONf_dihedral_angle_d15.0286232
X-RAY DIFFRACTIONf_chiral_restr0.0742605
X-RAY DIFFRACTIONf_plane_restr0.0052956
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1439X-RAY DIFFRACTIONPOSITIONAL
12B1439X-RAY DIFFRACTIONPOSITIONAL0.055
13C1438X-RAY DIFFRACTIONPOSITIONAL0.053
14D1385X-RAY DIFFRACTIONPOSITIONAL0.061
15E1417X-RAY DIFFRACTIONPOSITIONAL0.075
16F1420X-RAY DIFFRACTIONPOSITIONAL0.071
17G1405X-RAY DIFFRACTIONPOSITIONAL0.054
18H1406X-RAY DIFFRACTIONPOSITIONAL0.058
19I1451X-RAY DIFFRACTIONPOSITIONAL0.053
110J1416X-RAY DIFFRACTIONPOSITIONAL0.06
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.37441450.31482689X-RAY DIFFRACTION88
2.3261-2.35340.3231440.28752811X-RAY DIFFRACTION91
2.3534-2.38210.29771440.27912989X-RAY DIFFRACTION97
2.3821-2.41220.31271620.26793040X-RAY DIFFRACTION100
2.4122-2.44390.30161840.28613065X-RAY DIFFRACTION100
2.4439-2.47730.37451660.28233089X-RAY DIFFRACTION100
2.4773-2.51260.38321370.28273084X-RAY DIFFRACTION100
2.5126-2.55010.30391460.26073095X-RAY DIFFRACTION100
2.5501-2.58980.33711960.25833062X-RAY DIFFRACTION100
2.5898-2.63220.32431540.26653065X-RAY DIFFRACTION100
2.6322-2.67750.32721540.23513107X-RAY DIFFRACTION100
2.6775-2.72610.28721750.22963041X-RAY DIFFRACTION100
2.7261-2.77840.27871640.21863118X-RAY DIFFRACTION100
2.7784-2.83490.27621640.22513052X-RAY DIFFRACTION100
2.8349-2.89640.27451710.21153101X-RAY DIFFRACTION100
2.8964-2.96360.29441470.21193095X-RAY DIFFRACTION100
2.9636-3.03750.2441540.20433128X-RAY DIFFRACTION100
3.0375-3.11930.25491580.20933082X-RAY DIFFRACTION100
3.1193-3.21070.29891630.21013099X-RAY DIFFRACTION100
3.2107-3.31390.2931450.21513110X-RAY DIFFRACTION100
3.3139-3.43180.22431660.19373091X-RAY DIFFRACTION100
3.4318-3.56850.22521300.18343165X-RAY DIFFRACTION100
3.5685-3.72990.23041790.18593094X-RAY DIFFRACTION100
3.7299-3.92520.23261500.17493131X-RAY DIFFRACTION100
3.9252-4.16910.19281710.16313085X-RAY DIFFRACTION99
4.1691-4.48770.19431550.14943157X-RAY DIFFRACTION99
4.4877-4.93340.19681730.16053105X-RAY DIFFRACTION99
4.9334-5.63360.20851790.18113149X-RAY DIFFRACTION99
5.6336-7.04690.26861940.20963154X-RAY DIFFRACTION99
7.0469-20.15890.20181930.1923238X-RAY DIFFRACTION98

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