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- PDB-5afm: alpha7-AChBP in complex with lobeline and fragment 4 -

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Basic information

Entry
Database: PDB / ID: 5afm
Titlealpha7-AChBP in complex with lobeline and fragment 4
Components(ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA- ...) x 2
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 / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity ...sensory processing / dendrite arborization / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity / dendritic spine organization / acetylcholine binding / chloride channel regulator activity / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / plasma membrane raft / modulation of excitatory postsynaptic potential / response to amyloid-beta / monoatomic ion channel activity / negative regulation of tumor necrosis factor production / positive regulation of excitatory postsynaptic potential / toxic substance binding / monoatomic ion transport / positive regulation of protein metabolic process / positive regulation of long-term synaptic potentiation / response to nicotine / synapse organization / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / amyloid-beta binding / monoatomic ion transmembrane transport / postsynaptic membrane / postsynapse / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / learning or memory / response to hypoxia / neuron projection / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / synapse / 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
Chem-9Z0 / Alpha-Lobeline / Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
LYMNAEA STAGNALIS (great pond snail)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.85 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 / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: 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)124,63129
Polymers118,7335
Non-polymers5,89824
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.700, 119.600, 143.300
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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ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA- ... , 2 types, 5 molecules ACDEB

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


Mass: 23697.840 Da / Num. of mol.: 4
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: Protein ACETYLCHOLINE-BINDING PROTEIN, NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-7 / ALPHA7-ACHBP / ACH-BINDING PROTEIN / ACHBP


Mass: 23942.113 Da / Num. of mol.: 1
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 , 1 types, 10 molecules

#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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, 342 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-9Z0 / 4,5-dibromo-N-(3-hydroxypropyl)-1H-pyrrole-2-carboxamide


Mass: 325.985 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H10Br2N2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.08 % / 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: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 2.78→47.78 Å / Num. obs: 33519 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Biso Wilson estimate: 79.77 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11

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Processing

SoftwareName: BUSTER / Version: 2.8.0 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.85→47.72 Å / Cor.coef. Fo:Fc: 0.9396 / Cor.coef. Fo:Fc free: 0.9116 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 1554 5 %RANDOM
Rwork0.1614 ---
obs0.1642 31070 --
Displacement parametersBiso mean: 85.05 Å2
Baniso -1Baniso -2Baniso -3
1--22.1593 Å20 Å20 Å2
2--5.9269 Å20 Å2
3---16.2325 Å2
Refine analyzeLuzzati coordinate error obs: 0.392 Å
Refinement stepCycle: LAST / Resolution: 2.85→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8367 0 359 328 9054
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018967HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2812187HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2941SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes225HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1263HARMONIC5
X-RAY DIFFRACTIONt_it8762HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion23.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1132SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9889SEMIHARMONIC4
LS refinement shellResolution: 2.85→2.94 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2962 140 5.02 %
Rwork0.2042 2650 -
all0.2086 2790 -
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)
12.5431-0.25510.1963.2271-0.64133.183-0.02170.2425-0.0176-0.3818-0.1341-0.5178-0.62240.5020.15580.0014-0.03130.0507-0.2430.0158-0.335731.89985.528-35.0559
23.452-0.44030.26751.93960.09953.2264-0.0416-0.09240.3010.29260.0005-0.4218-1.08850.57440.0410.3895-0.2078-0.0679-0.416-0.0357-0.363635.745419.555-12.2949
31.2819-0.03850.35042.6368-1.27914.5339-0.0304-0.24410.07320.4278-0.0493-0.2209-0.90640.21780.07970.16640.0497-0.0015-0.3084-0.0861-0.369227.21014.17588.2847
42.7239-0.74210.52232.3161-0.05152.9165-0.1337-0.1538-0.38190.32380.24960.23210.1584-0.434-0.116-0.16240.02330.0908-0.18640.0505-0.153317.3675-18.8878-2.059
52.5329-1.9034-0.08773.1164-0.01044.08070.12790.0786-0.1404-0.5125-0.0190.08330.53-0.0961-0.1089-0.13210.0028-0.0168-0.2624-0.0471-0.201320.2394-18.1397-28.7228
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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