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- PDB-5afh: alpha7-AChBP in complex with lobeline -

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Basic information

Entry
Database: PDB / ID: 5afh
Titlealpha7-AChBP in complex with lobeline
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 receptor activity / acetylcholine-gated channel complex / short-term memory / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity / cation channel complex ...sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / short-term memory / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity / cation channel complex / dendritic spine organization / acetylcholine binding / chloride channel regulator activity / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / neurotransmitter receptor complex / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / modulation of excitatory postsynaptic potential / response to amyloid-beta / monoatomic ion channel activity / positive regulation of protein metabolic process / negative regulation of tumor necrosis factor production / plasma membrane raft / positive regulation of excitatory postsynaptic potential / toxic substance binding / monoatomic ion transport / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / positive regulation of long-term synaptic potentiation / regulation of membrane potential / excitatory postsynaptic potential / response to nicotine / synapse organization / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / transmembrane signaling receptor activity / amyloid-beta binding / monoatomic ion transmembrane transport / chemical synaptic transmission / postsynaptic membrane / learning or memory / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / postsynapse / positive regulation of MAPK cascade / neuron projection / positive regulation of cell population proliferation / synapse / dendrite / 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 transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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 transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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
Alpha-Lobeline / Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
LYMNAEA STAGNALIS (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 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 1.3Jun 10, 2015Group: Atomic model / Derived calculations / Other
Revision 1.4Mar 15, 2017Group: Source and taxonomy
Revision 1.5Apr 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 2.0Jul 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 / pdbx_validate_symm_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 / _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 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _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
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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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)122,62315
Polymers118,4895
Non-polymers4,13410
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.520, 112.504, 143.109
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, 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
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-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
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-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
#4: Chemical
ChemComp-L0B / Alpha-Lobeline


Mass: 337.455 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C22H27NO2 / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.91 Å3/Da / Density % sol: 57.66 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9194
DetectorType: ADSC CCD / Detector: CCD / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 2.7→48.59 Å / Num. obs: 38863 / % possible obs: 99.6 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Biso Wilson estimate: 52.85 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.7

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.4→44.223 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 2715 5 %
Rwork0.168 --
obs0.1709 54489 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→44.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8345 0 287 400 9032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098887
X-RAY DIFFRACTIONf_angle_d1.22912056
X-RAY DIFFRACTIONf_dihedral_angle_d16.423275
X-RAY DIFFRACTIONf_chiral_restr0.0461336
X-RAY DIFFRACTIONf_plane_restr0.0051515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44370.33791330.28552683X-RAY DIFFRACTION99
2.4437-2.49070.31681460.26862668X-RAY DIFFRACTION100
2.4907-2.54150.29471350.25752690X-RAY DIFFRACTION100
2.5415-2.59680.31971220.24342750X-RAY DIFFRACTION100
2.5968-2.65720.33971260.23982674X-RAY DIFFRACTION100
2.6572-2.72360.32931560.22542683X-RAY DIFFRACTION99
2.7236-2.79720.30321610.23932673X-RAY DIFFRACTION100
2.7972-2.87950.33261470.21342716X-RAY DIFFRACTION100
2.8795-2.97240.2511450.20192691X-RAY DIFFRACTION100
2.9724-3.07870.25761480.1882717X-RAY DIFFRACTION100
3.0787-3.20190.28911680.18982690X-RAY DIFFRACTION100
3.2019-3.34760.25491500.18052693X-RAY DIFFRACTION100
3.3476-3.5240.2671130.16732770X-RAY DIFFRACTION100
3.524-3.74470.22751330.15222728X-RAY DIFFRACTION100
3.7447-4.03360.20021320.14612767X-RAY DIFFRACTION100
4.0336-4.43920.16261300.12682741X-RAY DIFFRACTION100
4.4392-5.08080.1851730.12492747X-RAY DIFFRACTION100
5.0808-6.39810.20641450.15172790X-RAY DIFFRACTION100
6.3981-44.23030.17171520.16022903X-RAY DIFFRACTION99
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)
11.8733-0.43620.05152.02490.09982.3166-0.0134-0.10630.0654-0.00590.0355-0.2603-0.29520.2837-0.03860.3567-0.06330.02610.3393-0.00110.3359-2.013617.3819-16.2157
21.3902-0.0631-0.40411.8936-0.26072.4878-0.0733-0.2503-0.02050.23080.0346-0.0859-0.00910.11840.05920.3870.07530.01340.43890.00090.3306-11.45784.22245.5804
32.4032-0.44410.31591.85170.04731.7116-0.1507-0.2641-0.26820.19810.07620.23610.5463-0.19450.08280.4757-0.0150.15050.42740.02980.4505-24.5089-17.8872-3.0443
42.4355-1.0549-0.23091.91860.09932.4223-0.01160.138-0.238-0.1884-0.07610.170.3789-0.14420.07630.4021-0.06130.0170.3121-0.03050.3747-23.3708-18.6127-30.0144
51.6029-0.6484-0.35632.15960.14641.67690.00940.07090.0359-0.4244-0.0227-0.0784-0.06080.08070.01660.419-0.01040.01440.2911-0.00840.2974-9.57643.1782-38.2416
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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