[English] 日本語
Yorodumi
- PDB-5dsg: Structure of the M4 muscarinic acetylcholine receptor (M4-mT4L) b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dsg
TitleStructure of the M4 muscarinic acetylcholine receptor (M4-mT4L) bound to tiotropium
ComponentsMuscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4
KeywordsMEMBRANE PROTEIN / Membrane / GPCR / Signaling / Antagonist
Function / homology
Function and homology information


Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled serotonin receptor activity / regulation of locomotion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / viral release from host cell by cytolysis / peptidoglycan catabolic process / G protein-coupled acetylcholine receptor signaling pathway / cell wall macromolecule catabolic process ...Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled serotonin receptor activity / regulation of locomotion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / viral release from host cell by cytolysis / peptidoglycan catabolic process / G protein-coupled acetylcholine receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / host cell cytoplasm / cell surface receptor signaling pathway / defense response to bacterium / synapse / dendrite / signal transduction / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M4 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Muscarinic acetylcholine receptor M4 / Muscarinic acetylcholine receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-0HK / Chem-EDT / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-PG6 / Endolysin / Muscarinic acetylcholine receptor M4
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsThal, D.M. / Kobilka, B.K. / Sexton, P.M. / Christopoulos, A.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1055134 Australia
CitationJournal: Nature / Year: 2016
Title: Crystal structures of the M1 and M4 muscarinic acetylcholine receptors.
Authors: Thal, D.M. / Sun, B. / Feng, D. / Nawaratne, V. / Leach, K. / Felder, C.C. / Bures, M.G. / Evans, D.A. / Weis, W.I. / Bachhawat, P. / Kobilka, T.S. / Sexton, P.M. / Kobilka, B.K. / Christopoulos, A.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 13, 2024Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4
B: Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,70518
Polymers95,6012
Non-polymers5,10316
Water48627
1
A: Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,68510
Polymers47,8011
Non-polymers2,8849
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0208
Polymers47,8011
Non-polymers2,2197
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-9 kcal/mol
Surface area39120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.490, 172.040, 60.660
Angle α, β, γ (deg.)90.000, 94.370, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Muscarinic acetylcholine receptor M4,Endolysin,Endolysin,Muscarinic acetylcholine receptor M4 / Lysis protein / Lysozyme / Muramidase


Mass: 47800.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: CHRM4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08173, UniProt: P00720, lysozyme

-
Non-polymers , 7 types, 43 molecules

#2: Chemical ChemComp-0HK / (1R,2R,4S,5S,7S)-7-{[hydroxy(dithiophen-2-yl)acetyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane / Tiotropium


Mass: 392.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C19H22NO4S2 / Comment: antagonist*YM
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 64

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution: 20 - 40% PEG300, 100 mM MES, pH 5.5 - 7.5, and 10 - 150 mM EDTA, pH 8.0
PH range: 5.5 - 7.5

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2013
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: 2.6→28.99 Å / Num. obs: 30337 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Biso Wilson estimate: 55.88 Å2 / Rmerge F obs: 0.989 / Rmerge(I) obs: 0.213 / Rrim(I) all: 0.221 / Χ2: 1.009 / Net I/σ(I): 8.18 / Num. measured all: 397753
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.6-2.674.90.5410.9321.399993225822001.05397.4
2.67-2.740.6150.9931.7814735216421531.07799.5
2.74-2.820.7570.8652.4819477212721230.91999.8
2.82-2.910.8240.7913.2924506207520750.827100
2.91-30.8760.7223.9328260200520050.75100
3-3.110.8990.6194.7429038194619440.64199.9
3.11-3.220.9280.5185.6128366187318770.537100
3.22-3.360.9330.4426.5827167179517890.45899.7
3.36-3.510.9560.3667.9426309173617370.379100
3.51-3.680.9610.2999.5824889163016280.3199.9
3.68-3.880.970.25811.2623929156815690.268100
3.88-4.110.970.22313.0723198150115030.231100
4.11-4.390.9840.19114.6521627141214120.198100
4.39-4.750.9780.18115.5519677129512940.18899.9
4.75-5.20.9860.17615.3118108119111890.18499.8
5.2-5.810.9840.17314.8316855109310940.179100
5.81-6.710.9870.16315.11149759709690.16899.9
6.71-8.220.9960.11617.54120858098100.12100
8.22-11.630.9870.1219.8796666326310.12399.8
11.630.9950.10719.4848933623350.1192.5

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
PHASERphasing
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→28.53 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 2261 7.46 %
Rwork0.2265 28038 -
obs0.2275 30299 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.33 Å2 / Biso mean: 72.2251 Å2 / Biso min: 33.05 Å2
Refinement stepCycle: final / Resolution: 2.6→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6225 0 264 27 6516
Biso mean--79.42 51.1 -
Num. residues----793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026636
X-RAY DIFFRACTIONf_angle_d0.6138998
X-RAY DIFFRACTIONf_chiral_restr0.0221052
X-RAY DIFFRACTIONf_plane_restr0.0031084
X-RAY DIFFRACTIONf_dihedral_angle_d10.3242358
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3388X-RAY DIFFRACTION5.906TORSIONAL
12B3388X-RAY DIFFRACTION5.906TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.65650.31851430.29641684182797
2.6565-2.71830.3118970.289817951892100
2.7183-2.78620.31242030.271716631866100
2.7862-2.86150.27281010.250518121913100
2.8615-2.94560.27491420.258717241866100
2.9456-3.04050.30051600.260217811941100
3.0405-3.14910.30071020.262217471849100
3.1491-3.2750.31062010.254417061907100
3.275-3.42380.24891030.246418061909100
3.4238-3.6040.26211630.241417111874100
3.604-3.82930.25051390.222617821921100
3.8293-4.12420.2241030.215517851888100
4.1242-4.53770.20482000.203816951895100
4.5377-5.19090.25951030.214517971900100
5.1909-6.5270.26532000.245317121912100
6.527-28.53180.13021010.177618381939100
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)
11.4907-0.2725-0.31060.62010.220.6381-0.0553-0.10920.02320.09080.01690.11240.04260.03570.04180.5092-0.00770.03450.33970.01490.402649.55033.060868.4333
22.5492-2.56890.73063.6573-1.67291.40590.09570.0267-0.48080.83810.57452.225-0.4477-0.4868-0.54010.90710.07740.21890.60550.18251.424457.0988-42.106149.8993
34.2440.0028-2.34961.871-0.2994.40810.11310.0161-0.23640.2421-0.15360.41120.1191-0.27220.1430.4017-0.0237-0.09950.4663-0.06180.493942.53980.186461.6677
41.49520.01-0.16110.8195-0.2471.4918-0.0059-0.1789-0.02160.10190.0543-0.1421-0.2048-0.0195-0.04260.51490.0147-0.0170.3126-0.02330.359861.63826.089599.4122
53.34381.0872-0.29335.70571.24353.2083-0.2522-0.31680.08970.59590.09720.69570.3642-0.13140.10990.83310.0110.05580.4904-0.03260.827855.972251.909780.7578
62.44080.28290.96123.43041.43314.4728-0.0583-0.00680.3914-0.2226-0.1585-0.3072-0.26370.31870.26840.4531-0.03060.02850.43480.0760.556669.930110.445494.8941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 220 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 221 through 396 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 397 through 470 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 24 through 221 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 222 through 392 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 393 through 473 )B0

+
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