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- PDB-6kp6: The structural study of mutation induced inactivation of Human mu... -

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Basic information

Entry
Database: PDB / ID: 6kp6
TitleThe structural study of mutation induced inactivation of Human muscarinic receptor M4
ComponentsMuscarinic acetylcholine receptor M4,GlgA glycogen synthase,Muscarinic acetylcholine receptor M4
KeywordsMEMBRANE PROTEIN / muscarinic acetylcholine receptors / G protein-coupled receptors / M4 / mutation design / ligand screening
Function / homology
Function and homology information


Muscarinic acetylcholine receptors / glycogen (starch) synthase activity / G protein-coupled acetylcholine receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled serotonin receptor activity / glycogen biosynthetic process / regulation of locomotion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G protein-coupled acetylcholine receptor signaling pathway / G alpha (i) signalling events ...Muscarinic acetylcholine receptors / glycogen (starch) synthase activity / G protein-coupled acetylcholine receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled serotonin receptor activity / glycogen biosynthetic process / regulation of locomotion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G protein-coupled acetylcholine receptor signaling pathway / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / cell surface receptor signaling pathway / synapse / dendrite / signal transduction / plasma membrane / cytosol
Similarity search - Function
Muscarinic acetylcholine receptor M4 / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Muscarinic acetylcholine receptor family / Glycosyl transferases group 1 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Muscarinic acetylcholine receptor M4 / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Muscarinic acetylcholine receptor family / Glycosyl transferases group 1 / 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
Muscarinic acetylcholine receptor M4 / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWang, J.J. / Wu, M. / Wu, L.J. / Liu, Z.J. / Hua, T.
CitationJournal: Iucrj / Year: 2020
Title: The structural study of mutation-induced inactivation of human muscarinic receptor M4
Authors: Wang, J.J. / Wu, M. / Wu, L.J. / Xu, Y. / Li, F. / Wu, Y. / Popov, P. / Wang, L. / Bai, F. / Zhao, S. / Liu, Z.J. / Hua, T.
History
DepositionAug 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Muscarinic acetylcholine receptor M4,GlgA glycogen synthase,Muscarinic acetylcholine receptor M4


Theoretical massNumber of molelcules
Total (without water)55,4401
Polymers55,4401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23530 Å2
Unit cell
Length a, b, c (Å)56.100, 61.320, 203.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Muscarinic acetylcholine receptor M4,GlgA glycogen synthase,Muscarinic acetylcholine receptor M4 / Glycogen synthase


Mass: 55439.840 Da / Num. of mol.: 1 / Mutation: I93T G150A I187A S219Y N449R T459E
Source method: isolated from a genetically manipulated source
Details: fusion protein of Muscarinic acetylcholine receptor M4 and GlgA glycogen synthase
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi GE5 (archaea)
Gene: CHRM4, PAB2292 / Strain: GE5 / Orsay / Cell line (production host): insect cell / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08173, UniProt: Q9V2J8

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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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 7.8
Details: 300 mM diammonium hydrogen phosphate, 22-26% PEG 300, 0.1M HEPES sodium pH 7.6-8.2
PH range: 7.6-8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→49.14 Å / Num. obs: 14718 / % possible obs: 99.7 % / Redundancy: 27.108 % / Biso Wilson estimate: 89.34 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.118 / Χ2: 1.14 / Net I/σ(I): 19.32 / Num. measured all: 398969 / Scaling rejects: 235
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.086.0280.5862.36275107310410.3790.63797
3.08-3.169.1750.5873.089358102410200.5860.6299.6
3.16-3.2511.1380.5923.611305101510150.660.619100
3.25-3.3519.5990.5514.86193649889880.8590.565100
3.35-3.4626.2550.4766.56254949719710.9590.485100
3.46-3.5927.9350.3938.34257009209200.9780.4100
3.59-3.7230.6270.33210.97274428968960.990.338100
3.72-3.8732.050.27213.64274358568560.9940.276100
3.87-4.0532.4110.22916.78272588418410.9950.233100
4.05-4.2434.0680.19221.77270167937930.9960.195100
4.24-4.4733.9710.16725.1257167577570.9970.169100
4.47-4.7433.7940.13130.67248057347340.9990.133100
4.74-5.0736.2950.11833.352457267767710.12100
5.07-5.4835.6790.11432.022279963963910.115100
5.48-638.1410.11733.63224655895890.9990.118100
6-6.7138.0070.11336.07205245405400.9980.114100
6.71-7.7537.3310.08744.92182554894890.9990.088100
7.75-9.4935.2010.06157.431467941741710.062100
9.49-13.4235.9160.05664.541199633433410.057100
13.42-49.1432.3930.06260.2965112072010.9950.06497.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DSG

5dsg


Resolution: 3→49.14 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.392
RfactorNum. reflection% reflectionSelection details
Rfree0.264 731 4.97 %RANDOM
Rwork0.231 ---
obs0.233 14716 99.7 %-
Displacement parametersBiso max: 209.99 Å2 / Biso mean: 100.49 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.4922 Å20 Å20 Å2
2---3.0633 Å20 Å2
3---2.5712 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: final / Resolution: 3→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3711 0 0 0 3711
Num. residues----477
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1264SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes622HARMONIC5
X-RAY DIFFRACTIONt_it3799HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion514SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4384SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3799HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5171HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion20.32
LS refinement shellResolution: 3→3.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2954 142 4.84 %
Rwork0.2373 2793 -
all0.2401 2935 -
obs--98.62 %
Refinement TLS params.Method: refined / Origin x: -15.5423 Å / Origin y: 1.6557 Å / Origin z: -25.6893 Å
111213212223313233
T0.141 Å2-0.039 Å2-0.0167 Å2-0.0656 Å20.0436 Å2---0.3012 Å2
L0.4402 °20.0792 °20.675 °2-0.2666 °21.1374 °2--3.0393 °2
S0.0954 Å °-0.0298 Å °0.0375 Å °-0.0943 Å °-0.0165 Å °-0.0877 Å °0.1007 Å °0.0374 Å °-0.0788 Å °
Refinement TLS groupSelection details: { A|* }

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