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- PDB-3t4m: Ac-AChBP ligand binding domain mutated to human alpha-7 nAChR (in... -

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Basic information

Entry
Database: PDB / ID: 3t4m
TitleAc-AChBP ligand binding domain mutated to human alpha-7 nAChR (intermediate)
ComponentsSoluble acetylcholine receptor
KeywordsRECEPTOR / Mutated Acetylcholine Binding Protein / Aplysia californica / alpha-7 human nicotinic acetylcholine receptor / AChBP / nAChR / Binding Protein / Acetylcholine / Glycosylation
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / metal ion binding
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 / Mainly Beta
Similarity search - Domain/homology
Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNemecz, A. / Taylor, P.W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Creating an alpha-7 nicotinic acetylcholine recognition domain from the acetylcholine binding protein: crystallographic and ligand selectivity analyses
Authors: Nemecz, A. / Taylor, P.
History
DepositionJul 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble acetylcholine receptor
B: Soluble acetylcholine receptor
C: Soluble acetylcholine receptor
D: Soluble acetylcholine receptor
E: Soluble acetylcholine receptor
F: Soluble acetylcholine receptor
G: Soluble acetylcholine receptor
H: Soluble acetylcholine receptor
I: Soluble acetylcholine receptor
J: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,35331
Polymers263,47110
Non-polymers1,88221
Water1,63991
1
A: Soluble acetylcholine receptor
B: Soluble acetylcholine receptor
C: Soluble acetylcholine receptor
D: Soluble acetylcholine receptor
E: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,52715
Polymers131,7365
Non-polymers79110
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15720 Å2
ΔGint-160 kcal/mol
Surface area46300 Å2
MethodPISA
2
F: Soluble acetylcholine receptor
G: Soluble acetylcholine receptor
H: Soluble acetylcholine receptor
I: Soluble acetylcholine receptor
J: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,82616
Polymers131,7365
Non-polymers1,09111
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16650 Å2
ΔGint-170 kcal/mol
Surface area45920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.922, 152.220, 176.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 11 molecules ABCDEFGHIJ

#1: Protein
Soluble acetylcholine receptor


Mass: 26347.141 Da / Num. of mol.: 10 / Fragment: unp residues 18-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Gene: AChBP / Plasmid: pFLAG-CMV3 / Cell line (production host): HEK293S Gnt1 / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 111 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 0.02M calcium chloride, 30% 2-methyl-2,4-pentanediol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 56723 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 40.05 Å2 / Rmerge(I) obs: 0.22 / Rsym value: 0.22 / Net I/σ(I): 9.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 1.143 / Rsym value: 0.959 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CCP4Program Suite 6.1.3model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4Program Suite 6.1.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Modified 2-BYP

Resolution: 3→37.203 Å / SU ML: 0.33 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.27 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 2867 5.05 %Random 5.05% (2867 reflections)
Rwork0.1888 ---
all0.1914 56723 --
obs0.1914 56723 95.13 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.209 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.8525 Å2-0 Å20 Å2
2---2.5897 Å2-0 Å2
3---1.8897 Å2
Refinement stepCycle: LAST / Resolution: 3→37.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17201 0 111 91 17403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01417922
X-RAY DIFFRACTIONf_angle_d1.60124415
X-RAY DIFFRACTIONf_dihedral_angle_d17.1396645
X-RAY DIFFRACTIONf_chiral_restr0.1092665
X-RAY DIFFRACTIONf_plane_restr0.0093170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9979-3.04960.35851220.27982285X-RAY DIFFRACTION82
3.0496-3.1050.32571290.2532451X-RAY DIFFRACTION87
3.105-3.16470.31841240.2432480X-RAY DIFFRACTION89
3.1647-3.22930.29971520.22562529X-RAY DIFFRACTION91
3.2293-3.29950.3111240.21782603X-RAY DIFFRACTION92
3.2995-3.37620.29861350.20562577X-RAY DIFFRACTION93
3.3762-3.46050.24751280.19612682X-RAY DIFFRACTION95
3.4605-3.5540.26281370.18252672X-RAY DIFFRACTION96
3.554-3.65850.23221680.1772672X-RAY DIFFRACTION96
3.6585-3.77650.20041450.18112731X-RAY DIFFRACTION97
3.7765-3.91130.24361500.17672739X-RAY DIFFRACTION97
3.9113-4.06780.21491770.17312712X-RAY DIFFRACTION97
4.0678-4.25270.25141270.16792808X-RAY DIFFRACTION99
4.2527-4.47650.20691500.15282767X-RAY DIFFRACTION98
4.4765-4.75640.20881580.13912816X-RAY DIFFRACTION99
4.7564-5.12280.16821410.14362790X-RAY DIFFRACTION99
5.1228-5.63680.1911460.17822839X-RAY DIFFRACTION99
5.6368-6.44880.2581550.2072844X-RAY DIFFRACTION99
6.4488-8.11090.26871380.20742892X-RAY DIFFRACTION99
8.1109-37.20560.22661610.22212967X-RAY DIFFRACTION98

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