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- PDB-5afl: alpha7-AChBP in complex with lobeline and fragment 3 -

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Basic information

Entry
Database: PDB / ID: 5afl
Titlealpha7-AChBP in complex with lobeline and fragment 3
ComponentsACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7
KeywordsTRANSPORT PROTEIN / PENTAMERIC LIGAND-GATED ION CHANNELS / CYS-LOOP RECEPTOR / NICOTINIC ACETYLCHOLINE RECEPTOR / ALLOSTERIC MODULATION / DRUG DISCOVERY
Function / homology
Function and homology information


sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity / acetylcholine receptor activity / dendritic spine organization ...sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity / acetylcholine receptor activity / dendritic spine organization / acetylcholine binding / chloride channel regulator activity / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / acetylcholine-gated monoatomic cation-selective channel activity / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / plasma membrane raft / modulation of excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / response to amyloid-beta / negative regulation of tumor necrosis factor production / toxic substance binding / monoatomic ion transport / monoatomic ion transmembrane transport / positive regulation of protein metabolic process / positive regulation of long-term synaptic potentiation / synapse organization / response to nicotine / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / monoatomic ion channel activity / amyloid-beta binding / postsynapse / postsynaptic membrane / positive regulation of MAPK cascade / learning or memory / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / neuron projection / positive regulation of protein phosphorylation / synapse / positive regulation of cell population proliferation / signal transduction / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel ...Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / 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
N-(3-METHYLPHENYL)PYRROLIDINE-1-CARBOXAMIDE / Alpha-Lobeline / L(+)-TARTARIC ACID / Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
LYMNAEA STAGNALIS (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.385 Å
AuthorsSpurny, R. / Debaveye, S. / Farinha, A. / Veys, K. / Gossas, T. / Atack, J. / Bertrand, D. / Kemp, J. / Vos, A. / Danielson, U.H. ...Spurny, R. / Debaveye, S. / Farinha, A. / Veys, K. / Gossas, T. / Atack, J. / Bertrand, D. / Kemp, J. / Vos, A. / Danielson, U.H. / Tresadern, G. / Ulens, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Molecular Blueprint of Allosteric Binding Sites in a Homologue of the Agonist-Binding Domain of the Alpha7 Nicotinic Acetylcholine Receptor.
Authors: Spurny, R. / Debaveye, S. / Farinha, A. / Veys, K. / Vos, A.M. / Gossas, T. / Atack, J. / Bertrand, S. / Bertrand, D. / Danielson, U.H. / Tresadern, G. / Ulens, C.
History
DepositionJan 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2May 27, 2015Group: Database references
Revision 1.3Mar 15, 2017Group: Source and taxonomy
Revision 1.4Apr 24, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Sep 11, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_asym.entity_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7
B: ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7
C: ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7
D: ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7
E: ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,43822
Polymers118,4895
Non-polymers4,94817
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.808, 112.300, 143.720
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 , 1 types, 5 molecules ABCDE

#1: Protein
ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7 / ALPHA7-ACHBP / ACH-BINDING PROTEIN / ACHBP


Mass: 23697.840 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human), (gene. exp.) LYMNAEA STAGNALIS (great pond snail)
Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P36544*PLUS

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Sugars , 2 types, 5 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 243 molecules

#4: Chemical
ChemComp-L0B / Alpha-Lobeline


Mass: 337.455 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C22H27NO2 / Comment: alkaloid*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#7: Chemical ChemComp-FHV / N-(3-METHYLPHENYL)PYRROLIDINE-1-CARBOXAMIDE


Mass: 204.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N2O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHIMERIC PROTEIN BASED ON UNP ENTRIES P58154, P36544 MULTIPLE REGIONS OF THE CONSTRUCT EITHER ...CHIMERIC PROTEIN BASED ON UNP ENTRIES P58154, P36544 MULTIPLE REGIONS OF THE CONSTRUCT EITHER CORRESPOND TO HUMAN OR SNAIL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.91 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorDate: Apr 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.35→47.91 Å / Num. obs: 58398 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.8

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.385→41.829 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 2823 5.1 %
Rwork0.1708 --
obs0.1738 55675 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.385→41.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8355 0 342 231 8928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078968
X-RAY DIFFRACTIONf_angle_d1.12312161
X-RAY DIFFRACTIONf_dihedral_angle_d17.1723345
X-RAY DIFFRACTIONf_chiral_restr0.0741342
X-RAY DIFFRACTIONf_plane_restr0.0051529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3847-2.42580.31261330.25822447X-RAY DIFFRACTION94
2.4258-2.46990.35791440.27042604X-RAY DIFFRACTION100
2.4699-2.51740.39351600.26432603X-RAY DIFFRACTION100
2.5174-2.56880.29041390.25112624X-RAY DIFFRACTION100
2.5688-2.62460.30941320.23422635X-RAY DIFFRACTION100
2.6246-2.68570.28651550.23222628X-RAY DIFFRACTION100
2.6857-2.75280.33261190.22722654X-RAY DIFFRACTION100
2.7528-2.82720.30671340.21582637X-RAY DIFFRACTION100
2.8272-2.91040.29211280.20042639X-RAY DIFFRACTION100
2.9104-3.00430.26731540.1982631X-RAY DIFFRACTION100
3.0043-3.11160.2721420.18622636X-RAY DIFFRACTION100
3.1116-3.23620.26971440.18322651X-RAY DIFFRACTION100
3.2362-3.38340.26641410.17612634X-RAY DIFFRACTION100
3.3834-3.56170.19941430.16352667X-RAY DIFFRACTION100
3.5617-3.78470.21941390.14822659X-RAY DIFFRACTION100
3.7847-4.07670.24221480.15532659X-RAY DIFFRACTION100
4.0767-4.48650.17471470.13632674X-RAY DIFFRACTION99
4.4865-5.13480.19021420.13862674X-RAY DIFFRACTION99
5.1348-6.46540.21751360.16912706X-RAY DIFFRACTION99
6.4654-41.83550.18511430.15942790X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.26170.54060.34161.5540.24132.487-0.01260.2154-0.1491-0.03540.0605-0.15940.34850.2113-0.04380.38630.0713-0.01090.1925-0.00170.2145-1.9249-17.309716.1682
23.02270.99130.30372.4376-0.41692.8793-0.13020.3257-0.0205-0.34010.0744-0.04450.01460.14460.05690.3693-0.0524-0.02560.3527-0.01790.1712-11.5709-4.0081-5.6554
33.86481.22-0.58212.1211-0.08282.0642-0.09850.35880.3067-0.25030.04070.3713-0.6235-0.36190.06970.49860.0722-0.21020.43280.02110.4243-24.639118.06833.1831
43.2031.64620.03942.78820.08472.2919-0.0659-0.15660.3590.2256-0.07410.3812-0.5578-0.28890.04710.45420.0871-0.0010.2655-0.01660.3247-23.385818.763430.2732
52.12711.35230.45612.70040.08551.5450.1164-0.1003-0.02630.5752-0.1168-0.01020.0899-0.0238-0.00090.46980.03180.02330.2136-0.00520.1964-9.4734-3.116838.3077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

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