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- PDB-4u16: M3-mT4L receptor bound to NMS -

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Basic information

Entry
Database: PDB / ID: 4u16
TitleM3-mT4L receptor bound to NMS
ComponentsMuscarinic acetylcholine receptor M3,Lysozyme,Muscarinic acetylcholine receptor M3
KeywordsMEMBRANE PROTEIN/INHIBITOR / GPCR Crystallography T4 lysozyme / 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 / quaternary ammonium group binding / saliva secretion / G protein-coupled acetylcholine receptor activity / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / response to acetylcholine / positive regulation of vascular associated smooth muscle contraction / positive regulation of smooth muscle contraction ...negative regulation of heart rate by acetylcholine / G protein-coupled acetylcholine receptor binding / Muscarinic acetylcholine receptors / quaternary ammonium group binding / saliva secretion / G protein-coupled acetylcholine receptor activity / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / response to acetylcholine / positive regulation of vascular associated smooth muscle contraction / positive regulation of smooth muscle contraction / regulation of smooth muscle contraction / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / acetylcholine binding / synaptic transmission, cholinergic / G alpha (q) signalling events / acetylcholine receptor signaling pathway / positive regulation of vasoconstriction / ligand-gated ion channel signaling pathway / asymmetric synapse / smooth muscle contraction / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / viral release from host cell by cytolysis / peptidoglycan catabolic process / axon terminus / 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 / basolateral plasma membrane / chemical synaptic transmission / host cell cytoplasm / defense response to bacterium / synapse / dendrite / endoplasmic reticulum membrane / glutamatergic synapse / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M3 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. ...Muscarinic acetylcholine receptor M3 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / Lysozyme-like domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
N-methyl scopolamine / D(-)-TARTARIC 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: 3.7 Å
AuthorsThorsen, T.S. / Matt, R. / Weis, W.I. / Kobilka, B.
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 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)96,8037
Polymers95,7162
Non-polymers1,0875
Water00
1
A: Muscarinic acetylcholine receptor M3,Lysozyme,Muscarinic acetylcholine receptor M3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3263
Polymers47,8581
Non-polymers4682
Water0
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)48,4774
Polymers47,8581
Non-polymers6193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.391, 187.180, 53.548
Angle α, β, γ (deg.)90.00, 99.78, 90.00
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asym.

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Components

#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
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-3C0 / N-methyl scopolamine / (1R,2R,4S,5S,7s)-7-{[(2S)-3-hydroxy-2-phenylpropanoyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane


Mass: 318.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24NO4
Has protein modificationY
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: 4.24 Å3/Da / Density % sol: 70.96 %
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: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.7→33.7 Å / Num. obs: 14787 / % possible obs: 93.7 % / Redundancy: 2.6 % / Biso Wilson estimate: 119.14 Å2 / Rmerge(I) obs: 0.219 / Net I/σ(I): 8.9
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 2.2 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DAJ, 4LZM

4daj

4lzm


Resolution: 3.7→33.67 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2846 749 5.07 %
Rwork0.2386 --
obs0.2409 14787 92.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 76 0 5860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036009
X-RAY DIFFRACTIONf_angle_d0.5978251
X-RAY DIFFRACTIONf_dihedral_angle_d9.7562017
X-RAY DIFFRACTIONf_chiral_restr0.021000
X-RAY DIFFRACTIONf_plane_restr0.0031018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7001-3.98540.34331340.28382600X-RAY DIFFRACTION86
3.9854-4.38570.34061660.26632831X-RAY DIFFRACTION94
4.3857-5.01850.28371640.24062886X-RAY DIFFRACTION96
5.0185-6.31590.34671540.27622933X-RAY DIFFRACTION97
6.3159-33.67140.21881310.20092788X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -37.3762 Å / Origin y: -1.074 Å / Origin z: 5.547 Å
111213212223313233
T1.7924 Å2-0.0159 Å20.1948 Å2-0.7025 Å2-0.029 Å2--1.5777 Å2
L-0.2329 °2-0.6317 °2-0.1314 °2-5.1343 °2-0.2785 °2--0.6886 °2
S0.1183 Å °-0.0083 Å °-0.0679 Å °-0.6143 Å °-0.1295 Å °0.1124 Å °0.149 Å °0.0575 Å °0.0073 Å °
Refinement TLS groupSelection details: all

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