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- PDB-5cxv: Structure of the human M1 muscarinic acetylcholine receptor bound... -

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Basic information

Entry
Database: PDB / ID: 5cxv
TitleStructure of the human M1 muscarinic acetylcholine receptor bound to antagonist Tiotropium
Components
  • FLAG peptide
  • Muscarinic acetylcholine receptor M1,Endolysin,Muscarinic acetylcholine receptor M1
KeywordsHYDROLASE / Acetylcholine / Allosteric Regulation / Carrier Proteins / Cholinergic Antagonists / Tiotropium Receptor / Muscarinic M1 / GPCR / Subtype selectivity
Function / homology
Function and homology information


saliva secretion / regulation of glial cell proliferation / positive regulation of monoatomic ion transport / Muscarinic acetylcholine receptors / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled acetylcholine receptor activity / neuromuscular synaptic transmission / cholinergic synapse / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / positive regulation of intracellular protein transport ...saliva secretion / regulation of glial cell proliferation / positive regulation of monoatomic ion transport / Muscarinic acetylcholine receptors / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled acetylcholine receptor activity / neuromuscular synaptic transmission / cholinergic synapse / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / positive regulation of intracellular protein transport / phosphatidylinositol phospholipase C activity / G protein-coupled serotonin receptor activity / protein kinase C-activating G protein-coupled receptor signaling pathway / regulation of locomotion / postsynaptic modulation of chemical synaptic transmission / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / regulation of postsynaptic membrane potential / axon terminus / viral release from host cell by cytolysis / peptidoglycan catabolic process / postsynaptic density membrane / Schaffer collateral - CA1 synapse / G protein-coupled acetylcholine receptor signaling pathway / cognition / cell wall macromolecule catabolic process / lysozyme / presynaptic membrane / lysozyme activity / nervous system development / chemical synaptic transmission / G alpha (q) signalling events / host cell cytoplasm / defense response to bacterium / G protein-coupled receptor signaling pathway / dendrite / synapse / glutamatergic synapse / signal transduction / membrane / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M1 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM ...Muscarinic acetylcholine receptor M1 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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 / TRIETHYLENE GLYCOL / CHOLESTEROL HEMISUCCINATE / Endolysin / Muscarinic acetylcholine receptor M1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSun, B. / Feng, D. / Li, X. / Kobilka, T.S. / Kobilka, B.K.
CitationJournal: Nature / Year: 2016
Title: Crystal structures of the M1 and M4 muscarinic acetylcholine receptors.
Authors: Thal, D.M. / Sun, B. / Feng, D. / Nawaratne, V. / Leach, K. / Felder, C.C. / Bures, M.G. / Evans, D.A. / Weis, W.I. / Bachhawat, P. / Kobilka, T.S. / Sexton, P.M. / Kobilka, B.K. / Christopoulos, A.
History
DepositionJul 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Atomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Muscarinic acetylcholine receptor M1,Endolysin,Muscarinic acetylcholine receptor M1
C: FLAG peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8479
Polymers59,5392
Non-polymers1,3087
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint11 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.053, 72.186, 175.688
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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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Muscarinic acetylcholine receptor M1,Endolysin,Muscarinic acetylcholine receptor M1 / Lysis protein / Lysozyme / Muramidase


Mass: 58653.375 Da / Num. of mol.: 1
Mutation: N110Q, C1052T, C1095A,N110Q, C1052T, C1095A,N110Q, C1052T, C1095A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: CHRM1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11229, UniProt: P00720, lysozyme
#2: Protein/peptide FLAG peptide


Mass: 885.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T4 (virus)

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Non-polymers , 6 types, 17 molecules

#3: 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 / Tiotropium bromide


Mass: 392.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22NO4S2 / Comment: antagonist*YM
#4: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 33% PEG 300, 100 mM sodium acetate, and 100 mM Bis-Tris Propane (pH 8.0)
PH range: 8

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2011
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: 20402 / % possible obs: 97.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.155 / Χ2: 1.292 / Net I/av σ(I): 8.745 / Net I/σ(I): 7 / Num. measured all: 87751
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.84.20.83620391.01598.2
2.8-2.914.30.60620221.17898.3
2.91-3.044.40.48320181.29898.4
3.04-3.24.40.39320201.43697.6
3.2-3.44.30.29220191.35298.1
3.4-3.664.40.22120181.38697.1
3.66-4.034.40.16920341.36696.5
4.03-4.614.40.14220261.33596.4
4.61-5.84.30.12820761.25196.7
5.8-304.10.10921301.28594.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9 / SU B: 0.012 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28204 1011 5 %RANDOM
Rwork0.23133 ---
obs0.23384 19223 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 73.383 Å2
Baniso -1Baniso -2Baniso -3
1-3.31 Å20 Å20 Å2
2---0.85 Å20 Å2
3----2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3500 0 89 10 3599
LS refinement shellResolution: 2.698→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 63 -
Rwork0.319 1359 -
obs--92.4 %

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