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- PDB-6zg9: Structure of M1-StaR-T4L in complex with GSK1034702 at 2.5A -

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Basic information

Entry
Database: PDB / ID: 6zg9
TitleStructure of M1-StaR-T4L in complex with GSK1034702 at 2.5A
ComponentsMuscarinic acetylcholine receptor M1,Endolysin,Muscarinic acetylcholine receptor M1
KeywordsMEMBRANE PROTEIN / GPCR / 7TM
Function / homology
Function and homology information


saliva secretion / regulation of glial cell proliferation / positive regulation of monoatomic ion transport / 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 ...saliva secretion / regulation of glial cell proliferation / positive regulation of monoatomic ion transport / 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 / protein kinase C-activating G protein-coupled receptor signaling pathway / G protein-coupled serotonin receptor activity / 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 / lysozyme / presynaptic membrane / lysozyme activity / nervous system development / G alpha (q) signalling events / chemical synaptic transmission / host cell cytoplasm / defense response to bacterium / G protein-coupled receptor signaling pathway / glutamatergic synapse / synapse / dendrite / signal transduction / membrane / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M1 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM ...Muscarinic acetylcholine receptor M1 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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
OLEIC ACID / PHOSPHATE ION / Chem-QK2 / Endolysin / Muscarinic acetylcholine receptor M1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRucktooa, P. / Cooke, R.M.
CitationJournal: Cell / Year: 2021
Title: From structure to clinic: Design of a muscarinic M1 receptor agonist with potential to treatment of Alzheimer's disease.
Authors: Brown, A.J.H. / Bradley, S.J. / Marshall, F.H. / Brown, G.A. / Bennett, K.A. / Brown, J. / Cansfield, J.E. / Cross, D.M. / de Graaf, C. / Hudson, B.D. / Dwomoh, L. / Dias, J.M. / Errey, J.C. ...Authors: Brown, A.J.H. / Bradley, S.J. / Marshall, F.H. / Brown, G.A. / Bennett, K.A. / Brown, J. / Cansfield, J.E. / Cross, D.M. / de Graaf, C. / Hudson, B.D. / Dwomoh, L. / Dias, J.M. / Errey, J.C. / Hurrell, E. / Liptrot, J. / Mattedi, G. / Molloy, C. / Nathan, P.J. / Okrasa, K. / Osborne, G. / Patel, J.C. / Pickworth, M. / Robertson, N. / Shahabi, S. / Bundgaard, C. / Phillips, K. / Broad, L.M. / Goonawardena, A.V. / Morairty, S.R. / Browning, M. / Perini, F. / Dawson, G.R. / Deakin, J.F.W. / Smith, R.T. / Sexton, P.M. / Warneck, J. / Vinson, M. / Tasker, T. / Tehan, B.G. / Teobald, B. / Christopoulos, A. / Langmead, C.J. / Jazayeri, A. / Cooke, R.M. / Rucktooa, P. / Congreve, M.S. / Weir, M. / Tobin, A.B.
History
DepositionJun 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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,Muscarinic acetylcholine receptor M1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,19510
Polymers51,8331
Non-polymers2,3619
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint1 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.363, 66.571, 153.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 51833.414 Da / Num. of mol.: 1
Mutation: F27A,T32A,V46L,L64A,T95A,W101A,S112A,A143L,A196T,K362A,A364L,S411A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: CHRM1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11229, UniProt: P00720, lysozyme

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Non-polymers , 5 types, 32 molecules

#2: Chemical ChemComp-QK2 / 7-fluoranyl-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1~{H}-benzimidazol-2-one


Mass: 333.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24FN3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1 NaHEPES pH 7.4-7.8, 0.1M di-ammonium hydrogenohosphate, 30-38% PEG300
PH range: 7.4-7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.5→76.551 Å / Num. obs: 14062 / % possible obs: 91.2 % / Redundancy: 8.8 % / Rpim(I) all: 0.198 / Net I/σ(I): 4.8
Reflection shellResolution: 2.5→2.627 Å / Num. unique obs: 506 / Rpim(I) all: 1.857

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y00

2y00


Resolution: 2.5→33.97 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.853 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.36
RfactorNum. reflection% reflectionSelection details
Rfree0.242 732 5.21 %RANDOM
Rwork0.203 ---
obs0.205 14053 61.7 %-
Displacement parametersBiso max: 174.96 Å2 / Biso mean: 52.08 Å2 / Biso min: 5.46 Å2
Baniso -1Baniso -2Baniso -3
1--8.7331 Å20 Å20 Å2
2--18.0569 Å20 Å2
3----9.3238 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.5→33.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 159 23 3738
Biso mean--49.95 21.08 -
Num. residues----446
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1362SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes605HARMONIC5
X-RAY DIFFRACTIONt_it3794HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
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_contact4298SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3794HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg5124HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion19.9
LS refinement shellResolution: 2.5→2.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 36
RfactorNum. reflection% reflection
Rfree0.2527 16 4.09 %
Rwork0.2453 375 -
all0.2455 391 -
obs--16.06 %
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)
13.48370.3790.40270.4508-0.51584.8838-0.04250.10730.0543-0.0040.0172-0.008-0.1217-0.19970.0253-0.24920.03540.0320.0619-0.0184-0.2687-7.192516.2917-4.5396
23.2676-0.0737-0.54051.7647-0.98074.12-0.10.2555-0.2939-0.39070.12070.04160.04970.1026-0.0207-0.2889-0.063-0.00980.20880.0395-0.1948-17.475912.179-8.6403
36.5854-2.72391.5515.4411-2.95985.3098-0.3161-0.2087-0.0821-0.0107-0.0707-0.2831-0.14860.30160.3869-0.1939-0.1022-0.04970.20220.1685-0.4368-17.37336.8145-41.1458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|20 - 219 }A20 - 219
2X-RAY DIFFRACTION2{ A|354 - 439 }A354 - 439
3X-RAY DIFFRACTION3{ A|1002 - 1161 }A1002 - 1161

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