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- PDB-6zfz: Structure of M1-StaR-T4L in complex with 77-LH-28-1 at 2.17A -

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Basic information

Entry
Database: PDB / ID: 6zfz
TitleStructure of M1-StaR-T4L in complex with 77-LH-28-1 at 2.17A
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 / 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 / lysozyme activity / nervous system development / presynaptic membrane / 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 ...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 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / TRIETHYLENE GLYCOL / PHOSPHATE ION / Chem-QJT / Endolysin / Muscarinic acetylcholine receptor M1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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)55,41215
Polymers51,8331
Non-polymers3,57814
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-1 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.341, 65.631, 156.596
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 , 7 types, 47 molecules

#2: Chemical ChemComp-QJT / 1-[3-(4-butylpiperidin-1-yl)propyl]-3,4-dihydroquinolin-2-one


Mass: 328.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1M NaHEPES pH 7.4-7.8, 0.1M di-ammonium hydrogenphosphate, 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: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.17→50.3 Å / Num. obs: 25204 / % possible obs: 90.1 % / Redundancy: 5.5 % / Rpim(I) all: 0.114 / Net I/σ(I): 6
Reflection shellResolution: 2.17→2.344 Å / Num. unique obs: 908 / Rpim(I) all: 1.382

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Processing

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

2y00


Resolution: 2.17→50.3 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.324 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.317 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1194 4.74 %RANDOM
Rwork0.214 ---
obs0.215 25204 72.3 %-
Displacement parametersBiso max: 161.33 Å2 / Biso mean: 47.75 Å2 / Biso min: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.8527 Å20 Å20 Å2
2--5.5073 Å20 Å2
3----1.6546 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.17→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 249 33 3838
Biso mean--66.77 36 -
Num. residues----446
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1436SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes614HARMONIC5
X-RAY DIFFRACTIONt_it3896HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion491SEMIHARMONIC5
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_contact4330SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3896HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5232HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.22
X-RAY DIFFRACTIONt_other_torsion17.8
LS refinement shellResolution: 2.17→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.371 12 2.38 %
Rwork0.2318 493 -
all0.2346 505 -
obs--8.72 %
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)
11.7828-0.0483-0.20850.6279-0.162.1592-0.0063-0.2301-0.03840.0708-0.00720.0113-0.0064-0.02010.0135-0.1087-0.0095-0.0283-0.0055-0.0058-0.106920.874617.91936
25.60831.3782-0.8423.5569-1.37893.3624-0.18320.2866-0.1318-0.0311-0.1173-0.26970.23050.17430.3004-0.15040.07770.0434-0.12550.1079-0.30413.2308-3.051841.8884
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|20 - A|219 A|354 - A|439 }A20 - 219
2X-RAY DIFFRACTION1{ A|20 - A|219 A|354 - A|439 }A354 - 439
3X-RAY DIFFRACTION2{ A|1002 - A|1161 }A1002 - 1161

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