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- PDB-5zhp: M3 muscarinic acetylcholine receptor in complex with a selective ... -

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Basic information

Entry
Database: PDB / ID: 5zhp
TitleM3 muscarinic acetylcholine receptor in complex with a selective antagonist
ComponentsMuscarinic acetylcholine receptor M3,Endolysin,Endolysin,Muscarinic acetylcholine receptor M3
KeywordsMEMBRANE PROTEIN / G protein coupled receptor
Function / homology
Function and homology information


negative regulation of heart rate by acetylcholine / G protein-coupled acetylcholine receptor binding / Muscarinic acetylcholine receptors / regulation of vascular associated smooth muscle contraction / saliva secretion / quaternary ammonium group binding / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / response to acetylcholine / G protein-coupled acetylcholine receptor activity ...negative regulation of heart rate by acetylcholine / G protein-coupled acetylcholine receptor binding / Muscarinic acetylcholine receptors / regulation of vascular associated smooth muscle contraction / saliva secretion / quaternary ammonium group binding / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / response to acetylcholine / G protein-coupled acetylcholine receptor activity / positive regulation of vascular associated smooth muscle contraction / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / positive regulation of smooth muscle contraction / G protein-coupled serotonin receptor activity / synaptic transmission, cholinergic / acetylcholine binding / G alpha (q) signalling events / acetylcholine receptor signaling pathway / ligand-gated ion channel signaling pathway / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / asymmetric synapse / smooth muscle contraction / axon terminus / viral release from host cell by cytolysis / positive regulation of vasoconstriction / peptidoglycan catabolic process / basal plasma membrane / calcium-mediated signaling / postsynaptic density membrane / positive regulation of insulin secretion / G protein-coupled acetylcholine receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / presynaptic membrane / chemical synaptic transmission / basolateral plasma membrane / host cell cytoplasm / defense response to bacterium / glutamatergic synapse / synapse / dendrite / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M3 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Muscarinic acetylcholine receptor M3 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
alpha-maltose / Chem-9EC / CITRIC ACID / Endolysin / Muscarinic acetylcholine receptor M3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLiu, H. / Hofmann, J. / Fish, I. / Schaake, B. / Eitel, K. / Bartuschat, A. / Kaindl, J. / Rampp, H. / Banerjee, A. / Hubner, H. ...Liu, H. / Hofmann, J. / Fish, I. / Schaake, B. / Eitel, K. / Bartuschat, A. / Kaindl, J. / Rampp, H. / Banerjee, A. / Hubner, H. / Clark, M.J. / Vincent, S.G. / Fisher, J. / Heinrich, M. / Hirata, K. / Liu, X. / Sunahara, R.K. / Shoichet, B.K. / Kobilka, B.K. / Gmeiner, P.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
US National Institutes of HealthGM106990 United States
German Research FoundationGm 13/10 and GRK 1910 Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists
Authors: Liu, H. / Hofmann, J. / Fish, I. / Schaake, B. / Eitel, K. / Bartuschat, A. / Kaindl, J. / Rampp, H. / Banerjee, A. / Hubner, H. / Clark, M.J. / Vincent, S.G. / Fisher, J.T. / Heinrich, M.R. ...Authors: Liu, H. / Hofmann, J. / Fish, I. / Schaake, B. / Eitel, K. / Bartuschat, A. / Kaindl, J. / Rampp, H. / Banerjee, A. / Hubner, H. / Clark, M.J. / Vincent, S.G. / Fisher, J.T. / Heinrich, M.R. / Hirata, K. / Liu, X. / Sunahara, R.K. / Shoichet, B.K. / Kobilka, B.K. / Gmeiner, P.
History
DepositionMar 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: 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: Muscarinic acetylcholine receptor M3,Endolysin,Endolysin,Muscarinic acetylcholine receptor M3
B: Muscarinic acetylcholine receptor M3,Endolysin,Endolysin,Muscarinic acetylcholine receptor M3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6468
Polymers95,8562
Non-polymers1,7906
Water00
1
A: Muscarinic acetylcholine receptor M3,Endolysin,Endolysin,Muscarinic acetylcholine receptor M3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8544
Polymers47,9281
Non-polymers9263
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20320 Å2
MethodPISA
2
B: Muscarinic acetylcholine receptor M3,Endolysin,Endolysin,Muscarinic acetylcholine receptor M3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7924
Polymers47,9281
Non-polymers8643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-1 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.110, 53.050, 124.720
Angle α, β, γ (deg.)90.00, 98.70, 90.00
Int Tables number3
Space group name H-MP121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Muscarinic acetylcholine receptor M3,Endolysin,Endolysin,Muscarinic acetylcholine receptor M3 / Lysis protein / Lysozyme / Muramidase


Mass: 47928.141 Da / Num. of mol.: 2 / Mutation: S154R,C1054A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: Chrm3, Chrm-3, e / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08483, UniProt: D9IEF7, lysozyme
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 5 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-9EC / (1R,2R,4S,5S,7s)-7-({[4-fluoro-2-(thiophen-2-yl)phenyl]carbamoyl}oxy)-9,9-dimethyl-3-oxa-9-azatricyclo[3.3.1.0~2,4~]nonan-9-ium


Mass: 389.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22FN2O3S
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7

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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: 4.17 Å3/Da / Density % sol: 70.47 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 40-43% PEG300, 300-400 mM ammonium citrate, 0.1M tris-HCI, pH7.5, 1mM 6o,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 29106 / % possible obs: 99.3 % / Redundancy: 8.4 % / CC1/2: 0.99 / Net I/σ(I): 6.63
Reflection shellResolution: 3.1→3.2 Å / Mean I/σ(I) obs: 1.03 / Num. unique obs: 2511 / CC1/2: 0.536 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U15

4u15


Resolution: 3.1→19.984 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 2184 7.57 %
Rwork0.2291 --
obs0.232 28842 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→19.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 122 0 6324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026488
X-RAY DIFFRACTIONf_angle_d0.478865
X-RAY DIFFRACTIONf_dihedral_angle_d12.7523718
X-RAY DIFFRACTIONf_chiral_restr0.3111039
X-RAY DIFFRACTIONf_plane_restr0.0021077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.16720.34081480.34531567X-RAY DIFFRACTION96
3.1672-3.24050.37791280.32931601X-RAY DIFFRACTION96
3.2405-3.32120.36481160.30631679X-RAY DIFFRACTION98
3.3212-3.41060.31691280.31091607X-RAY DIFFRACTION99
3.4106-3.51040.37011400.28481673X-RAY DIFFRACTION99
3.5104-3.62310.28981410.26831621X-RAY DIFFRACTION99
3.6231-3.75180.27421420.24721684X-RAY DIFFRACTION100
3.7518-3.90090.29041330.24431663X-RAY DIFFRACTION100
3.9009-4.0770.25451310.24531694X-RAY DIFFRACTION100
4.077-4.290.28311330.22341666X-RAY DIFFRACTION100
4.29-4.55580.25011590.20571652X-RAY DIFFRACTION100
4.5558-4.90270.22191340.20031688X-RAY DIFFRACTION100
4.9027-5.38730.24841390.2151685X-RAY DIFFRACTION100
5.3873-6.14690.27691550.24991678X-RAY DIFFRACTION99
6.1469-7.67090.2881250.22321737X-RAY DIFFRACTION100
7.6709-19.98460.20421320.16891763X-RAY DIFFRACTION99

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