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- PDB-5yc8: Crystal structure of rationally thermostabilized M2 muscarinic ac... -

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Basic information

Entry
Database: PDB / ID: 5yc8
TitleCrystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with NMS (Hg-derivative)
ComponentsMuscarinic acetylcholine receptor M2,Redesigned apo-cytochrome b562,Muscarinic acetylcholine receptor M2
KeywordsMEMBRANE PROTEIN / GPCR crystallography / rationally thermostabilized mutant
Function / homology
Function and homology information


Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / cholinergic synapse / regulation of smooth muscle contraction / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / arrestin family protein binding / regulation of heart contraction / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / presynaptic modulation of chemical synaptic transmission ...Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / cholinergic synapse / regulation of smooth muscle contraction / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / arrestin family protein binding / regulation of heart contraction / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / presynaptic modulation of chemical synaptic transmission / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to virus / G protein-coupled acetylcholine receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / nervous system development / presynapse / Clathrin-mediated endocytosis / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / cilium / ciliary basal body / G protein-coupled receptor signaling pathway / synapse / dendrite / nucleolus / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M2 / Muscarinic acetylcholine receptor family / 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)
Similarity search - Domain/homology
N-methyl scopolamine / : / Muscarinic acetylcholine receptor M2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsSuno, R. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. ...Suno, R. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. / Yamamoto, M. / Kobilka, B.K. / Iwata, S. / Kobayashi, T.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Structural insights into the subtype-selective antagonist binding to the M2muscarinic receptor
Authors: Suno, R. / Lee, S. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. / Yamamoto, M. / Kobilka, B.K. / ...Authors: Suno, R. / Lee, S. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. / Yamamoto, M. / Kobilka, B.K. / Vaidehi, N. / Iwata, S. / Kobayashi, T.
History
DepositionSep 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 26, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Muscarinic acetylcholine receptor M2,Redesigned apo-cytochrome b562,Muscarinic acetylcholine receptor M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2135
Polymers47,2931
Non-polymers9204
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-54 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.520, 59.000, 89.220
Angle α, β, γ (deg.)90.000, 98.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Muscarinic acetylcholine receptor M2,Redesigned apo-cytochrome b562,Muscarinic acetylcholine receptor M2


Mass: 47293.207 Da / Num. of mol.: 1 / Fragment: UNP residues 10-214,UNP residues 377-466 / Mutation: S110R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRM2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08172
#2: 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.: 1 / Source method: obtained synthetically / Formula: C18H24NO4
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 50mM MES-NaOH pH 6.2-7.0, 26-32% PEG300, 300~500mM Ammonium Fluoride, 1% 1,2,3-heptanetriol, 0.5mM NMS and 5% DMSO, 1mM HgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→49.03 Å / Num. obs: 32428 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.491 % / Biso Wilson estimate: 36.98 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.487 / Rrim(I) all: 0.508 / Χ2: 1.184 / Net I/σ(I): 7.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.6512.1034.9791.0651820.4385.19799.9
2.65-2.8312.3492.7091.6648870.642.825100
2.83-3.0612.491.5272.5446700.8011.591100.1
3.06-3.3512.6170.8854.0242350.8940.92299.9
3.35-3.7412.6070.4696.9837700.9680.489100
3.74-4.3212.6610.23712.8533920.9860.24899.9
4.32-5.2812.6870.17517.3328620.9920.18299.9
5.28-7.4312.7170.15817.8922050.9930.165100
7.43-49.0312.5710.09627.9612250.9970.199.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5XBB

5xbb
PDB Unreleased entry


Resolution: 2.5→49.03 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.23
RfactorNum. reflection% reflection
Rfree0.2703 1728 5.33 %
Rwork0.2371 --
obs0.2388 32414 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.55 Å2 / Biso mean: 63.5492 Å2 / Biso min: 19.94 Å2
Refinement stepCycle: final / Resolution: 2.5→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 26 22 3090
Biso mean--40.9 39.51 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023144
X-RAY DIFFRACTIONf_angle_d0.4914291
X-RAY DIFFRACTIONf_chiral_restr0.036511
X-RAY DIFFRACTIONf_plane_restr0.004518
X-RAY DIFFRACTIONf_dihedral_angle_d11.471887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5001-2.57370.29531490.315125612710
2.5737-2.65680.36261410.297625442685
2.6568-2.75170.32511400.281125752715
2.7517-2.86190.29251430.266825172660
2.8619-2.99210.24051400.253825812721
2.9921-3.14980.28681520.253425872739
3.1498-3.34710.3041380.249925632701
3.3471-3.60550.29091490.243725412690
3.6055-3.96820.21671390.214725772716
3.9682-4.54210.23851490.206725392688
4.5421-5.72110.34911530.234225442697
5.7211-49.03990.20021350.205325572692
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)
12.9517-1.324-0.05091.9012-0.93725.0678-0.0339-0.01970.03790.18060.08760.0369-0.0855-0.0135-0.04910.2299-0.00630.04190.1279-0.03190.3072171.279435.5983533.1464
21.0286-0.0534-0.53543.1597-1.51752.2668-0.045-0.1159-0.00890.1431-0.0691-0.1798-0.07750.48210.12470.1814-0.0266-0.00930.3444-0.03060.3042189.354331.5579531.8703
39.24110.26722.3514.944.14783.9767-0.5545-1.4465-0.19920.8484-0.2629-0.36910.5828-0.17050.40970.31280.2139-0.04140.2423-0.04640.4094187.291214.5998542.8896
42.53510.3312-3.18852.54312.31196.9746-0.47810.18430.6829-0.00440.5962-0.61680.34290.974-0.11491.03570.1233-0.09561.2940.20480.6365171.408915.6593564.9558
55.8933-0.88191.3873.9776-0.71415.0177-0.5176-1.0348-1.052-0.24230.9351-0.10270.05960.0059-0.39131.15230.11940.01591.07240.13350.6809170.888512.142572.0083
63.551-0.14040.16271.15170.87481.04960.19890.1491-0.146-0.35010.43980.35191.2204-0.6321-0.29121.2812-0.2015-0.29332.02070.60490.8937166.2813.0564579.2525
72.6101-0.0292.62632.24360.62092.85670.1238-1.5875-0.26520.5571-0.04350.1469-0.2252-0.4471-0.13391.0513-0.0653-0.02721.18390.03820.8708163.925720.7694573.7725
84.71660.1995-1.12944.77-0.48196.7199-0.0327-0.4238-0.09820.24610.05830.0064-0.2774-0.1065-0.0170.17570.0157-0.02220.13050.01320.3089179.228119.6999536.7767
91.988-0.5002-2.07773.96723.55097.7310.0086-0.28130.03120.3112-0.08820.1573-0.0459-0.04880.11040.2861-0.0422-0.05040.29060.0640.3238171.224928.8013536.3583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 92 )A16 - 92
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 195 )A93 - 195
3X-RAY DIFFRACTION3chain 'A' and (resid 196 through 213 )A196 - 213
4X-RAY DIFFRACTION4chain 'A' and (resid 214 or (resid 1001 through 1018 ))A214 - 1018
5X-RAY DIFFRACTION5chain 'A' and (resid 1019 through 1055 )A1019 - 1055
6X-RAY DIFFRACTION6chain 'A' and (resid 1056 through 1080 )A1056 - 1080
7X-RAY DIFFRACTION7chain 'A' and ((resid 1081 through 1106) or (resid 380 through 380) )A1081 - 380
8X-RAY DIFFRACTION8chain 'A' and (resid 381 through 411 )A381 - 411
9X-RAY DIFFRACTION9chain 'A' and (resid 412 through 458 )A412 - 458

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