[English] 日本語
Yorodumi
- PDB-4daj: Structure of the M3 Muscarinic Acetylcholine Receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4daj
TitleStructure of the M3 Muscarinic Acetylcholine Receptor
ComponentsMuscarinic acetylcholine receptor M3, Lysozyme
KeywordsSIGNALING PROTEIN / Hydrolase / G protein-coupled receptor / muscarinic receptor / Acetylcholine receptor
Function / homology
Function and homology information


negative regulation of heart rate by acetylcholine / G protein-coupled acetylcholine receptor binding / Muscarinic acetylcholine receptors / regulation of vascular associated smooth muscle contraction / saliva secretion / quaternary ammonium group binding / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / response to acetylcholine / G protein-coupled acetylcholine receptor activity ...negative regulation of heart rate by acetylcholine / G protein-coupled acetylcholine receptor binding / Muscarinic acetylcholine receptors / regulation of vascular associated smooth muscle contraction / saliva secretion / quaternary ammonium group binding / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / response to acetylcholine / G protein-coupled acetylcholine receptor activity / positive regulation of vascular associated smooth muscle contraction / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / positive regulation of smooth muscle contraction / G protein-coupled serotonin receptor activity / synaptic transmission, cholinergic / G alpha (q) signalling events / acetylcholine binding / acetylcholine receptor signaling pathway / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / ligand-gated ion channel signaling pathway / asymmetric synapse / smooth muscle contraction / axon terminus / positive regulation of vasoconstriction / viral release from host cell by cytolysis / peptidoglycan catabolic process / basal plasma membrane / calcium-mediated signaling / postsynaptic density membrane / G protein-coupled acetylcholine receptor signaling pathway / positive regulation of insulin secretion / cell wall macromolecule catabolic process / presynaptic membrane / lysozyme / lysozyme activity / chemical synaptic transmission / basolateral plasma membrane / host cell cytoplasm / defense response to bacterium / dendrite / glutamatergic synapse / synapse / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M3 / Muscarinic acetylcholine receptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme ...Muscarinic acetylcholine receptor M3 / Muscarinic acetylcholine receptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-0HK / PHOSPHATE ION / Endolysin / Muscarinic acetylcholine receptor M3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsKruse, A.C. / Hu, J. / Pan, A.C. / Arlow, D.H. / Rosenbaum, D.M. / Rosemond, E. / Green, H.F. / Liu, T. / Chae, P.S. / Dror, R.O. ...Kruse, A.C. / Hu, J. / Pan, A.C. / Arlow, D.H. / Rosenbaum, D.M. / Rosemond, E. / Green, H.F. / Liu, T. / Chae, P.S. / Dror, R.O. / Shaw, D.E. / Weis, W.I. / Wess, J. / Kobilka, B.
CitationJournal: Nature / Year: 2012
Title: Structure and dynamics of the M3 muscarinic acetylcholine receptor.
Authors: Kruse, A.C. / Hu, J. / Pan, A.C. / Arlow, D.H. / Rosenbaum, D.M. / Rosemond, E. / Green, H.F. / Liu, T. / Chae, P.S. / Dror, R.O. / Shaw, D.E. / Weis, W.I. / Wess, J. / Kobilka, B.K.
History
DepositionJan 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Muscarinic acetylcholine receptor M3, Lysozyme
B: Muscarinic acetylcholine receptor M3, Lysozyme
C: Muscarinic acetylcholine receptor M3, Lysozyme
D: Muscarinic acetylcholine receptor M3, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,48118
Polymers219,9614
Non-polymers2,52014
Water0
1
A: Muscarinic acetylcholine receptor M3, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7636
Polymers54,9901
Non-polymers7725
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Muscarinic acetylcholine receptor M3, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4783
Polymers54,9901
Non-polymers4872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Muscarinic acetylcholine receptor M3, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5734
Polymers54,9901
Non-polymers5823
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Muscarinic acetylcholine receptor M3, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6685
Polymers54,9901
Non-polymers6774
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Muscarinic acetylcholine receptor M3, Lysozyme
B: Muscarinic acetylcholine receptor M3, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2409
Polymers109,9812
Non-polymers1,2607
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-37 kcal/mol
Surface area41180 Å2
MethodPISA
6
C: Muscarinic acetylcholine receptor M3, Lysozyme
D: Muscarinic acetylcholine receptor M3, Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2409
Polymers109,9812
Non-polymers1,2607
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-37 kcal/mol
Surface area41060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.770, 61.310, 176.910
Angle α, β, γ (deg.)85.87, 89.90, 84.90
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Muscarinic acetylcholine receptor M3, Lysozyme / Endolysin / Lysis protein / Muramidase


Mass: 54990.297 Da / Num. of mol.: 4
Fragment: P08483 residues 57-259, 482-589, P00720 residues 1-161
Mutation: C1054T, C1097A
Source method: isolated from a genetically manipulated source
Details: Chimeric Protein
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: Chrm-3, Chrm3, E / Plasmid: PVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P08483, UniProt: P00720, lysozyme
#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 / Tiotropium bromide


Mass: 392.512 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H22NO4S2 / Comment: antagonist*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 76

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 27-38% PEG 300, 100 mM HEPES pH 7.5, 1% (w/w) 1,2,3-heptanetriol, and 100 mM ammonium phosphate. Protein was reconstituted in cubic phase using a 10:1 monolein:cholesterol mix by weight, ...Details: 27-38% PEG 300, 100 mM HEPES pH 7.5, 1% (w/w) 1,2,3-heptanetriol, and 100 mM ammonium phosphate. Protein was reconstituted in cubic phase using a 10:1 monolein:cholesterol mix by weight, Lipidic cubic phase, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1781
2781
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.033
SYNCHROTRONAPS 23-ID-D21.033
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDAug 14, 2011mirrors
MARMOSAIC 300 mm CCD2CCDAug 23, 2011mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.4→40 Å / Num. obs: 28385 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.226 / Net I/σ(I): 4.5
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.7 / % possible all: 85.9

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: M2 muscarinic acetylcholine receptor (3UON)

3uon


Resolution: 3.4→39.9 Å / SU ML: 0.59 / σ(F): 1.98 / Phase error: 33.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.303 1276 4.91 %
Rwork0.251 --
obs0.254 26013 82.9 %
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.36 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1698 Å22.0178 Å20.1059 Å2
2--6.5992 Å2-1.3222 Å2
3----4.4294 Å2
Refinement stepCycle: LAST / Resolution: 3.4→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13435 0 154 0 13589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114794
X-RAY DIFFRACTIONf_angle_d0.86219010
X-RAY DIFFRACTIONf_dihedral_angle_d14.7224824
X-RAY DIFFRACTIONf_chiral_restr0.0582248
X-RAY DIFFRACTIONf_plane_restr0.0032303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.53610.4295930.33671695X-RAY DIFFRACTION52
3.5361-3.6970.33981140.31552116X-RAY DIFFRACTION64
3.697-3.89170.36351140.29622535X-RAY DIFFRACTION75
3.8917-4.13530.34471390.27332882X-RAY DIFFRACTION87
4.1353-4.45420.3271580.23983039X-RAY DIFFRACTION91
4.4542-4.90180.27531610.21283052X-RAY DIFFRACTION92
4.9018-5.60940.28491550.24383132X-RAY DIFFRACTION94
5.6094-7.06080.35411680.28433102X-RAY DIFFRACTION94
7.0608-39.90650.23581740.21793184X-RAY DIFFRACTION96

+
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://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