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- PDB-4mqs: Structure of active human M2 muscarinic acetylcholine receptor bo... -

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Basic information

Entry
Database: PDB / ID: 4mqs
TitleStructure of active human M2 muscarinic acetylcholine receptor bound to the agonist iperoxo
Components
  • Muscarinic acetylcholine receptor M2
  • Nanobody 9-8
KeywordsSIGNALING PROTEIN / G protein-coupled receptor / Muscarinic acetylcholine receptor
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 / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / regulation of smooth muscle contraction / 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 / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / regulation of smooth muscle contraction / 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 / dendrite / synapse / nucleolus / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M2 / Muscarinic acetylcholine receptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) ...Muscarinic acetylcholine receptor M2 / Muscarinic acetylcholine receptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-IXO / Muscarinic acetylcholine receptor M2
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKruse, A.C. / Ring, A.M. / Manglik, A. / Hu, J. / Hu, K. / Eitel, K. / Huebner, H. / Pardon, E. / Valant, C. / Sexton, P.M. ...Kruse, A.C. / Ring, A.M. / Manglik, A. / Hu, J. / Hu, K. / Eitel, K. / Huebner, H. / Pardon, E. / Valant, C. / Sexton, P.M. / Christopoulos, A. / Felder, C.C. / Gmeiner, P. / Steyaert, J. / Weis, W.I. / Garcia, K.C. / Wess, J. / Kobilka, B.K.
CitationJournal: Nature / Year: 2013
Title: Activation and allosteric modulation of a muscarinic acetylcholine receptor.
Authors: Kruse, A.C. / Ring, A.M. / Manglik, A. / Hu, J. / Hu, K. / Eitel, K. / Hubner, H. / Pardon, E. / Valant, C. / Sexton, P.M. / Christopoulos, A. / Felder, C.C. / Gmeiner, P. / Steyaert, J. / ...Authors: Kruse, A.C. / Ring, A.M. / Manglik, A. / Hu, J. / Hu, K. / Eitel, K. / Hubner, H. / Pardon, E. / Valant, C. / Sexton, P.M. / Christopoulos, A. / Felder, C.C. / Gmeiner, P. / Steyaert, J. / Weis, W.I. / Garcia, K.C. / Wess, J. / Kobilka, B.K.
History
DepositionSep 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Jul 5, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Muscarinic acetylcholine receptor M2
B: Nanobody 9-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5773
Polymers53,3802
Non-polymers1971
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-15 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.896, 78.130, 163.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Muscarinic acetylcholine receptor M2


Mass: 39951.734 Da / Num. of mol.: 1 / Fragment: UNP residues 1-232, 373-466 / Mutation: N0D, N1D, N4D, N7D, A373T, K374R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRM2 / Plasmid: PVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08172
#2: Antibody Nanobody 9-8


Mass: 13428.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pMAL3CBN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical ChemComp-IXO / 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium / Iperoxo


Mass: 197.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O2
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: 3.76 Å3/Da / Density % sol: 67.31 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution: 10 - 20% PEG300, 100 mM HEPES, pH 7.2 - 7.9, 1.2% 1,2,3-heptanetriol, and 20 - 80 mM EDTA, pH 8.0, Lipidic cubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2013 / Details: mirrors
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: 3.5→33 Å / Num. all: 10386 / Num. obs: 10386 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.188
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.744 / Num. unique all: 871 / % possible all: 83.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1241)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UON

3uon


Resolution: 3.5→32.522 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 35.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2982 1030 10.06 %Random
Rwork0.2493 ---
obs0.2544 10237 96.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→32.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3020 0 14 0 3034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043125
X-RAY DIFFRACTIONf_angle_d0.8614290
X-RAY DIFFRACTIONf_dihedral_angle_d14.1531026
X-RAY DIFFRACTIONf_chiral_restr0.061508
X-RAY DIFFRACTIONf_plane_restr0.004526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.68430.39751290.34421129X-RAY DIFFRACTION86
3.6843-3.91480.36061460.29641300X-RAY DIFFRACTION96
3.9148-4.21650.34161490.27071318X-RAY DIFFRACTION99
4.2165-4.63970.33341480.22961327X-RAY DIFFRACTION98
4.6397-5.30860.28071510.2211346X-RAY DIFFRACTION98
5.3086-6.67870.29321480.27211365X-RAY DIFFRACTION98
6.6787-32.52320.2431590.22081422X-RAY DIFFRACTION97

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