[English] 日本語
Yorodumi
- PDB-6zg4: Structure of M1-StaR-T4L in complex with HTL0009936 at 2.35A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zg4
TitleStructure of M1-StaR-T4L in complex with HTL0009936 at 2.35A
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 / presynaptic membrane / 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 / TRIETHYLENE GLYCOL / PHOSPHATE ION / Chem-QK8 / Endolysin / Muscarinic acetylcholine receptor M1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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: 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.pdbx_database_id_DOI / _citation.title / _citation.year
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Muscarinic acetylcholine receptor M1,Endolysin,Muscarinic acetylcholine receptor M1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,74117
Polymers51,8331
Non-polymers3,90816
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-6 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.47, 65.45, 154.83
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

-
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

-
Non-polymers , 5 types, 88 molecules

#2: Chemical ChemComp-QK8 / ethyl (4~{S})-4-[4-[(1-methylcyclobutyl)carbamoyl]piperidin-1-yl]azepane-1-carboxylate


Mass: 365.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H35N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.72 %
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

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.03319 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.353→49.982 Å / Num. obs: 20575 / % possible obs: 89.2 % / Redundancy: 5.9 % / Rpim(I) all: 0.194 / Net I/σ(I): 7.1
Reflection shellResolution: 2.353→2.484 Å / Num. unique obs: 674 / Rpim(I) all: 1.525

-
Processing

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

2y00


Resolution: 2.33→49.98 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.882 / SU R Cruickshank DPI: 0.463 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.464 / SU Rfree Blow DPI: 0.258 / SU Rfree Cruickshank DPI: 0.261
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1000 -RANDOM
Rwork0.204 ---
obs0.205 20579 74 %-
Displacement parametersBiso mean: 35.72 Å2
Baniso -1Baniso -2Baniso -3
1--3.2656 Å20 Å20 Å2
2--8.658 Å20 Å2
3----5.3923 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.33→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 271 72 3899
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093894HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.975220HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1432SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes609HARMONIC5
X-RAY DIFFRACTIONt_it3894HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4518SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion18.66
LS refinement shellResolution: 2.33→2.45 Å
RfactorNum. reflection% reflection
Rfree0.2842 18 -
Rwork0.2283 --
obs0.2305 412 10.92 %
Refinement TLS params.

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)
11.64930.0767-0.10550.59130.27442.3764-0.0303-0.0252-0.0005-0.02520.02010.0823-0.00050.08230.0102-0.120.0115-0.0190.02770.0069-0.1697-21.044218.0776-5.9288
25.5623-1.1915-0.76732.98490.43943.2862-0.37970.0530.25680.0530.0597-0.01630.2568-0.01630.3201-0.0839-0.04160.0162-0.093-0.1041-0.3298-13.3869-3.3031-41.5044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|20 - A|219 A|354 - A|439 }
2X-RAY DIFFRACTION2{ A|1002 - A|1161 }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more