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- PDB-4u15: M3-mT4L receptor bound to tiotropium -

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Basic information

Entry
Database: PDB / ID: 4u15
TitleM3-mT4L receptor bound to tiotropium
ComponentsMuscarinic acetylcholine receptor M3,Lysozyme,Muscarinic acetylcholine receptor M3
KeywordsMEMBRANE PROTEIN/INHIBITOR / GPCR T4L Stabillized Crystallography / MEMBRANE PROTEIN / MEMBRANE PROTEIN-INHIBITOR complex
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
Chem-0HK / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / D(-)-TARTARIC ACID / Endolysin / Muscarinic acetylcholine receptor M3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsThorsen, T.S. / Matt, R. / Weis, W.I. / Kobilka, B.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Benzon foundation Denmark
CitationJournal: Structure / Year: 2014
Title: Modified T4 Lysozyme Fusion Proteins Facilitate G Protein-Coupled Receptor Crystallogenesis.
Authors: Thorsen, T.S. / Matt, R. / Weis, W.I. / Kobilka, B.K.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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,Lysozyme,Muscarinic acetylcholine receptor M3
B: Muscarinic acetylcholine receptor M3,Lysozyme,Muscarinic acetylcholine receptor M3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,94414
Polymers95,7162
Non-polymers3,22812
Water181
1
A: Muscarinic acetylcholine receptor M3,Lysozyme,Muscarinic acetylcholine receptor M3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3987
Polymers47,8581
Non-polymers1,5406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Muscarinic acetylcholine receptor M3,Lysozyme,Muscarinic acetylcholine receptor M3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5467
Polymers47,8581
Non-polymers1,6886
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-21 kcal/mol
Surface area36890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.311, 184.563, 52.613
Angle α, β, γ (deg.)90.00, 98.54, 90.00
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Muscarinic acetylcholine receptor M3,Lysozyme,Muscarinic acetylcholine receptor M3


Mass: 47858.023 Da / Num. of mol.: 2
Fragment: UNP P08483 residues 57-259, 482-563, UNP D9IEF7 residues 61-161
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, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08483, UniProt: D9IEF7, lysozyme

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Non-polymers , 5 types, 13 molecules

#2: Chemical ChemComp-0HK / (1R,2R,4S,5S,7S)-7-{[hydroxy(dithiophen-2-yl)acetyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane / Tiotropium


Mass: 392.512 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22NO4S2 / Comment: antagonist*YM
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C4H6O6
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe fusion protein is a chimeric of M3 and RB69 lysozyme. The fusion protein is made of M 3 ( ...The fusion protein is a chimeric of M3 and RB69 lysozyme. The fusion protein is made of M 3 ( residues 57-259) - Lysozyme (residues 1000-1117)- M3 (residues 482-563).

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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: 3.81 Å3/Da / Density % sol: 67.72 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: The best crystallization condition was 100 mM Tris pH 7.5, 44% PEG 300 and 400 mM ammonium tartrate.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 37934 / % possible obs: 96.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 73.91 Å2 / Rmerge(I) obs: 0.129 / Χ2: 0.997 / Net I/av σ(I): 10.05 / Net I/σ(I): 8.6 / Num. measured all: 193093
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.7-2.76424680.98893.2
2.76-2.834.523950.99893.6
2.83-2.914.624941.011940.941
2.91-2.994.824941.03495.70.789
2.99-3.095.125811.05997.90.663
3.09-3.25.425301.01898.10.551
3.2-3.335.525861.02998.20.418
3.33-3.485.525611.04798.10.319
3.48-3.665.525421.00397.90.234
3.66-3.895.525591.04697.90.171
3.89-4.195.425710.99797.50.139
4.19-4.615.225470.97896.80.1
4.61-5.285.125640.93197.20.082
5.28-6.645.325570.91196.70.087
6.64-30524850.89893.90.057

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
DENZOdata reduction
RefinementResolution: 2.8→28.477 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 33.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 1703 4.99 %
Rwork0.23 --
obs0.2316 34101 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→28.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6123 0 218 1 6342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036495
X-RAY DIFFRACTIONf_angle_d0.6568837
X-RAY DIFFRACTIONf_dihedral_angle_d13.4492293
X-RAY DIFFRACTIONf_chiral_restr0.0211029
X-RAY DIFFRACTIONf_plane_restr0.0031071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.88240.40331400.3882576X-RAY DIFFRACTION94
2.8824-2.97530.42931420.36282653X-RAY DIFFRACTION95
2.9753-3.08150.33821420.31462758X-RAY DIFFRACTION98
3.0815-3.20470.34051420.28872689X-RAY DIFFRACTION98
3.2047-3.35040.29491450.27112724X-RAY DIFFRACTION98
3.3504-3.52670.32491450.24762758X-RAY DIFFRACTION98
3.5267-3.74720.26491410.22842733X-RAY DIFFRACTION98
3.7472-4.03580.25991420.22542713X-RAY DIFFRACTION98
4.0358-4.44060.23821390.20652703X-RAY DIFFRACTION97
4.4406-5.080.28391420.20042709X-RAY DIFFRACTION97
5.08-6.38830.2421430.24382718X-RAY DIFFRACTION97
6.3883-28.47820.18691400.1832664X-RAY DIFFRACTION94

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