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- PDB-5dsg: Structure of the M4 muscarinic acetylcholine receptor (M4-mT4L) b... -

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Basic information

Entry
Database: PDB / ID: 5dsg
TitleStructure of the M4 muscarinic acetylcholine receptor (M4-mT4L) bound to tiotropium
ComponentsMuscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4
KeywordsMEMBRANE PROTEIN / Membrane / GPCR / Signaling / Antagonist
Function / homology
Function and homology information


Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled serotonin receptor activity / regulation of locomotion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / viral release from host cell by cytolysis / peptidoglycan catabolic process / G protein-coupled acetylcholine receptor signaling pathway / cell wall macromolecule catabolic process ...Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled serotonin receptor activity / regulation of locomotion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / viral release from host cell by cytolysis / peptidoglycan catabolic process / G protein-coupled acetylcholine receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / host cell cytoplasm / cell surface receptor signaling pathway / defense response to bacterium / dendrite / synapse / signal transduction / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M4 / 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 M4 / 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. / 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 / Chem-EDT / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-PG6 / Endolysin / Muscarinic acetylcholine receptor M4
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsThal, D.M. / Kobilka, B.K. / Sexton, P.M. / Christopoulos, A.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1055134 Australia
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
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 13, 2024Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4
B: Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,70518
Polymers95,6012
Non-polymers5,10316
Water48627
1
A: Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,68510
Polymers47,8011
Non-polymers2,8849
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0208
Polymers47,8011
Non-polymers2,2197
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-9 kcal/mol
Surface area39120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.490, 172.040, 60.660
Angle α, β, γ (deg.)90.000, 94.370, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4 / Lysis protein / Lysozyme / Muramidase


Mass: 47800.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: CHRM4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08173, UniProt: P00720, lysozyme

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Non-polymers , 7 types, 43 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: isolated from a genetically manipulated source
Formula: C19H22NO4S2 / Comment: antagonist*YM
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 64

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution: 20 - 40% PEG300, 100 mM MES, pH 5.5 - 7.5, and 10 - 150 mM EDTA, pH 8.0
PH range: 5.5 - 7.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2013
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→28.99 Å / Num. obs: 30337 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Biso Wilson estimate: 55.88 Å2 / Rmerge F obs: 0.989 / Rmerge(I) obs: 0.213 / Rrim(I) all: 0.221 / Χ2: 1.009 / Net I/σ(I): 8.18 / Num. measured all: 397753
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.6-2.674.90.5410.9321.399993225822001.05397.4
2.67-2.740.6150.9931.7814735216421531.07799.5
2.74-2.820.7570.8652.4819477212721230.91999.8
2.82-2.910.8240.7913.2924506207520750.827100
2.91-30.8760.7223.9328260200520050.75100
3-3.110.8990.6194.7429038194619440.64199.9
3.11-3.220.9280.5185.6128366187318770.537100
3.22-3.360.9330.4426.5827167179517890.45899.7
3.36-3.510.9560.3667.9426309173617370.379100
3.51-3.680.9610.2999.5824889163016280.3199.9
3.68-3.880.970.25811.2623929156815690.268100
3.88-4.110.970.22313.0723198150115030.231100
4.11-4.390.9840.19114.6521627141214120.198100
4.39-4.750.9780.18115.5519677129512940.18899.9
4.75-5.20.9860.17615.3118108119111890.18499.8
5.2-5.810.9840.17314.8316855109310940.179100
5.81-6.710.9870.16315.11149759709690.16899.9
6.71-8.220.9960.11617.54120858098100.12100
8.22-11.630.9870.1219.8796666326310.12399.8
11.630.9950.10719.4848933623350.1192.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
PHASERphasing
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→28.53 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 2261 7.46 %
Rwork0.2265 28038 -
obs0.2275 30299 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.33 Å2 / Biso mean: 72.2251 Å2 / Biso min: 33.05 Å2
Refinement stepCycle: final / Resolution: 2.6→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6225 0 264 27 6516
Biso mean--79.42 51.1 -
Num. residues----793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026636
X-RAY DIFFRACTIONf_angle_d0.6138998
X-RAY DIFFRACTIONf_chiral_restr0.0221052
X-RAY DIFFRACTIONf_plane_restr0.0031084
X-RAY DIFFRACTIONf_dihedral_angle_d10.3242358
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3388X-RAY DIFFRACTION5.906TORSIONAL
12B3388X-RAY DIFFRACTION5.906TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.65650.31851430.29641684182797
2.6565-2.71830.3118970.289817951892100
2.7183-2.78620.31242030.271716631866100
2.7862-2.86150.27281010.250518121913100
2.8615-2.94560.27491420.258717241866100
2.9456-3.04050.30051600.260217811941100
3.0405-3.14910.30071020.262217471849100
3.1491-3.2750.31062010.254417061907100
3.275-3.42380.24891030.246418061909100
3.4238-3.6040.26211630.241417111874100
3.604-3.82930.25051390.222617821921100
3.8293-4.12420.2241030.215517851888100
4.1242-4.53770.20482000.203816951895100
4.5377-5.19090.25951030.214517971900100
5.1909-6.5270.26532000.245317121912100
6.527-28.53180.13021010.177618381939100
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)
11.4907-0.2725-0.31060.62010.220.6381-0.0553-0.10920.02320.09080.01690.11240.04260.03570.04180.5092-0.00770.03450.33970.01490.402649.55033.060868.4333
22.5492-2.56890.73063.6573-1.67291.40590.09570.0267-0.48080.83810.57452.225-0.4477-0.4868-0.54010.90710.07740.21890.60550.18251.424457.0988-42.106149.8993
34.2440.0028-2.34961.871-0.2994.40810.11310.0161-0.23640.2421-0.15360.41120.1191-0.27220.1430.4017-0.0237-0.09950.4663-0.06180.493942.53980.186461.6677
41.49520.01-0.16110.8195-0.2471.4918-0.0059-0.1789-0.02160.10190.0543-0.1421-0.2048-0.0195-0.04260.51490.0147-0.0170.3126-0.02330.359861.63826.089599.4122
53.34381.0872-0.29335.70571.24353.2083-0.2522-0.31680.08970.59590.09720.69570.3642-0.13140.10990.83310.0110.05580.4904-0.03260.827855.972251.909780.7578
62.44080.28290.96123.43041.43314.4728-0.0583-0.00680.3914-0.2226-0.1585-0.3072-0.26370.31870.26840.4531-0.03060.02850.43480.0760.556669.930110.445494.8941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 220 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 221 through 396 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 397 through 470 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 24 through 221 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 222 through 392 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 393 through 473 )B0

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