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- PDB-6wjc: Muscarinic acetylcholine receptor 1 - muscarinic toxin 7 complex -

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Basic information

Entry
Database: PDB / ID: 6wjc
TitleMuscarinic acetylcholine receptor 1 - muscarinic toxin 7 complex
Components
  • Muscarinic acetylcholine receptor M1,Endolysin fusion
  • Muscarinic toxin 7
KeywordsMEMBRANE PROTEIN / GPCR / natural toxin
Function / homology
Function and homology information


saliva secretion / regulation of glial cell proliferation / positive regulation of monoatomic ion transport / receptor antagonist activity / 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 ...saliva secretion / regulation of glial cell proliferation / positive regulation of monoatomic ion transport / receptor antagonist activity / 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 / presynaptic membrane / lysozyme / lysozyme activity / nervous system development / toxin activity / chemical synaptic transmission / G alpha (q) signalling events / host cell cytoplasm / defense response to bacterium / G protein-coupled receptor signaling pathway / dendrite / glutamatergic synapse / synapse / signal transduction / extracellular region / membrane / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M1 / Muscarinic acetylcholine receptor family / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Endolysin T4 type / T4-type lysozyme ...Muscarinic acetylcholine receptor M1 / Muscarinic acetylcholine receptor family / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / G-protein coupled receptors family 1 signature. / Ribbon / 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 / Mainly Beta
Similarity search - Domain/homology
ACETAMIDE / Chem-OIN / CHOLESTEROL HEMISUCCINATE / Endolysin / Muscarinic acetylcholine receptor M1 / Muscarinic toxin 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
Dendroaspis angusticeps (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMaeda, S. / Kobilka, B.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM083118 United States
CitationJournal: Science / Year: 2020
Title: Structure and selectivity engineering of the M1muscarinic receptor toxin complex.
Authors: Maeda, S. / Xu, J. / N Kadji, F.M. / Clark, M.J. / Zhao, J. / Tsutsumi, N. / Aoki, J. / Sunahara, R.K. / Inoue, A. / Garcia, K.C. / Kobilka, B.K.
History
DepositionApr 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 18, 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

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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 fusion
C: Muscarinic toxin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9908
Polymers64,6952
Non-polymers2,2956
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, pharmacological assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-3 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.148, 150.429, 76.927
Angle α, β, γ (deg.)90.000, 98.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AC

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


Mass: 56907.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: CHRM1, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11229, UniProt: D9IEF7, lysozyme
#2: Protein Muscarinic toxin 7 / MT7 / Muscarinic toxin 1 / m1-toxin


Mass: 7787.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendroaspis angusticeps (eastern green mamba)
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8QGR0

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Non-polymers , 4 types, 13 molecules

#3: Chemical ChemComp-ACM / ACETAMIDE / Acetamide


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#4: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-OIN / (1R,5S)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL (2R)-3-HYDROXY-2-PHENYLPROPANOATE / ATROPINE / Atropine


Mass: 289.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, alkaloid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22-27% SOKALAN, HEPES(7.5), 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.55→46.31 Å / Num. obs: 44412 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.026 / Rrim(I) all: 0.048 / Net I/σ(I): 12.4 / Num. measured all: 149894 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.55-2.653.51.0931639446640.6490.6821.2911.299.9
9.54-46.313.20.0226398230.9990.0130.02435.894

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSVERSION Jan 26, 2018data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CXV, 2VLW

5cxv

2vlw


Resolution: 2.55→44.11 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2626 1997 4.5 %
Rwork0.2445 42349 -
obs0.2453 44346 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 229.03 Å2 / Biso mean: 123.9659 Å2 / Biso min: 58.18 Å2
Refinement stepCycle: final / Resolution: 2.55→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4041 0 165 7 4213
Biso mean--142.34 103.33 -
Num. residues----514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.610.45451430.476330263169100
2.61-2.680.47541430.451330453188100
2.68-2.760.4721430.435430253168100
2.76-2.850.50631430.382930283171100
2.85-2.950.41621430.351630133156100
2.95-3.070.39261420.329230363178100
3.07-3.210.3851430.311930193162100
3.21-3.380.28051430.286930373180100
3.38-3.590.30341440.26263043318799
3.59-3.870.25271380.26412953309197
3.87-4.260.24291420.21173010315299
4.26-4.880.21651440.19923048319299
4.88-6.140.24761430.23173035317899
6.14-44.110.20931430.20233031317498
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)
14.5721-1.7351-0.11280.9084-1.10075.0992-0.23250.34640.02010.3635-0.0194-1.1833-0.07810.13080.15390.82210.027-0.15710.5314-0.06211.20268.865129.21881.6213
23.2695-0.57581.52370.67721.00133.4122-0.30160.25920.3595-0.24440.1153-0.0201-0.38760.40280.13820.6111-0.1006-0.00550.54410.06561.054125.581722.6029-0.1616
34.0827-0.4081-0.01741.34830.25345.2304-0.4206-0.07620.447-0.20620.0650.288-0.39520.00520.29650.9733-0.0704-0.24470.76440.01131.562144.11750.215129.3401
45.2253.0924-0.36212.22190.43812.296-0.1633-0.16350.0954-1.0391-0.4185-0.8394-0.152-0.06830.6310.751-0.06470.07080.60770.01680.276721.045522.572713.5449
57.00353.76640.97438.5929-3.1246.0509-0.4881-0.14551.2585-0.40420.1617-0.4105-0.5997-0.17860.31560.5029-0.02280.00850.7019-0.0451.035312.129529.84587.1791
68.84697.77975.40257.04595.13224.00811.17960.1587-0.62681.7918-0.3519-2.69742.35231.9268-0.74941.52960.2698-0.47440.8082-0.19251.893128.4864-20.7685-13.4884
76.9851-3.8963-4.08413.72383.64573.74070.1816-0.302-1.43640.70230.3688-1.02350.43922.3483-0.58241.17650.1552-0.21091.2459-0.16341.372531.944-7.1579-7.1824
89.1039-6.262-1.15354.30820.87533.676-0.02680.618-1.22661.8275-0.42481.18861.38640.7450.44461.45490.232-0.16990.7521-0.05991.832523.0405-14.8998-5.5463
95.5471-1.7634-3.63725.59796.95629.06370.11710.01590.09471.4979-0.1309-0.4817-0.74111.16510.0041.1390.1158-00.6001-0.18911.748316.44252.73182.3528
105.55374.3504-2.6683.8444-2.83533.5776-0.3017-0.0846-0.90031.4960.6674-0.78151.2907-0.3518-0.27291.26430.1867-0.36070.9079-0.15781.80222.969-10.7631-3.7265
115.1968-4.9325-1.36994.9199-0.10489.6765-1.4873-0.96960.72560.94610.7708-0.25821.7947-0.42020.81791.1321-0.01430.12950.90190.03452.154312.462-6.67561.0015
125.9287-4.93-4.64224.10073.86123.6392-0.11061.5639-1.6055-0.13660.23441.39151.4575-0.3625-0.15461.43850.1704-0.08651.0848-0.12542.005122.5449-12.7633-13.0452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 17:57)A17 - 57
2X-RAY DIFFRACTION2(chain A and resid 58:207)A58 - 207
3X-RAY DIFFRACTION3(chain A and resid 208:218)A208 - 218
4X-RAY DIFFRACTION4(chain A and resid 386:414)A386 - 414
5X-RAY DIFFRACTION5(chain A and resid 415:461)A415 - 461
6X-RAY DIFFRACTION6(chain A and resid 219:221)A219 - 221
7X-RAY DIFFRACTION7(chain A and resid 222:235)A222 - 235
8X-RAY DIFFRACTION8(chain A and resid 236:246)A236 - 246
9X-RAY DIFFRACTION9(chain A and resid 247:254)A247 - 254
10X-RAY DIFFRACTION10(chain A and resid 255:264)A255 - 264
11X-RAY DIFFRACTION11(chain A and resid 265:273)A265 - 273
12X-RAY DIFFRACTION12(chain A and resid 274:283)A274 - 283

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