[English] 日本語
Yorodumi
- PDB-5zkb: Crystal structure of rationally thermostabilized M2 muscarinic ac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zkb
TitleCrystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with AF-DX 384
ComponentsMuscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2
KeywordsMEMBRANE PROTEIN/INHIBITOR / GPCR crystallography / rationally thermostabilized mutant / MEMBRANE PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


Muscarinic acetylcholine receptors / symmetric synapse / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled acetylcholine receptor activity / regulation of smooth muscle contraction / cholinergic synapse / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled serotonin receptor activity / arrestin family protein binding / regulation of heart contraction ...Muscarinic acetylcholine receptors / symmetric synapse / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled acetylcholine receptor activity / regulation of smooth muscle contraction / cholinergic synapse / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled serotonin receptor activity / arrestin family protein binding / regulation of heart contraction / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / asymmetric synapse / axon terminus / presynaptic modulation of chemical synaptic transmission / clathrin-coated endocytic vesicle membrane / response to virus / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / Clathrin-mediated endocytosis / nervous system development / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / G protein-coupled receptor signaling pathway / neuronal cell body / dendrite / synapse / glutamatergic synapse / membrane / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M2 / Muscarinic acetylcholine receptor family / 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)
Similarity search - Domain/homology
Chem-82F / Muscarinic acetylcholine receptor M2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSuno, R. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. ...Suno, R. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. / Yamamoto, M. / Kobilka, B.K. / Iwata, S. / Kobayashi, T.
Funding support Japan, United States, 6items
OrganizationGrant numberCountry
Japan Science and TechnologyThe Research Acceleration Program Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)The Platform Project for Supporting Drug Discovery and Life Science Research Japan
Japan Society for the Promotion of ScienceInternational Collaboration in Chemistry Japan
Japan Agency for Medical Research and Development (AMED)The Platform Project for Supporting Drug Discovery and Life Science Research Japan
Japan Society for the Promotion of Science15K08268, 15H06862 Japan
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)NIH R01-GM097261 United States
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Structural insights into the subtype-selective antagonist binding to the M2muscarinic receptor
Authors: Suno, R. / Lee, S. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. / Yamamoto, M. / Kobilka, B.K. / ...Authors: Suno, R. / Lee, S. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. / Yamamoto, M. / Kobilka, B.K. / Vaidehi, N. / Iwata, S. / Kobayashi, T.
History
DepositionMar 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7722
Polymers47,2931
Non-polymers4791
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21070 Å2
Unit cell
Length a, b, c (Å)213.010, 60.090, 48.750
Angle α, β, γ (deg.)90.00, 92.66, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2


Mass: 47293.207 Da / Num. of mol.: 1 / Fragment: UNP residues 10-217,UNP residues 377-466 / Mutation: S110R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRM2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08172
#2: Chemical ChemComp-82F / N-[2-[(2S)-2-[(dipropylamino)methyl]piperidin-1-yl]ethyl]-6-oxidanylidene-5H-pyrido[2,3-b][1,4]benzodiazepine-11-carboxamide


Mass: 478.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38N6O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 50mM MES-NaOH pH 6.2-7.0, 18 % PEG300, 100mM Magnesium acetate, 1% 1,2,3-heptanetriol, 0.5mM AF-DX 384 and 5% DMSO

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 13188 / % possible obs: 100 % / Redundancy: 18.1 % / Net I/σ(I): 8.08
Reflection shellResolution: 2.95→3.13 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→48.697 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.22
RfactorNum. reflection% reflection
Rfree0.2795 661 5.01 %
Rwork0.2297 --
obs0.2321 13188 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→48.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 35 0 3058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023137
X-RAY DIFFRACTIONf_angle_d0.4754275
X-RAY DIFFRACTIONf_dihedral_angle_d12.7391870
X-RAY DIFFRACTIONf_chiral_restr0.037503
X-RAY DIFFRACTIONf_plane_restr0.003530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.17780.34011360.28092486X-RAY DIFFRACTION100
3.1778-3.49750.31051330.25352488X-RAY DIFFRACTION100
3.4975-4.00340.25721290.21992476X-RAY DIFFRACTION100
4.0034-5.0430.28711290.21512505X-RAY DIFFRACTION100
5.043-48.7040.23661340.21272572X-RAY DIFFRACTION100
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)
11.4421.7204-0.38413.56740.21240.40020.5227-0.0794-0.61530.6806-0.2751-0.79370.06671.127-0.2890.62690.1381-0.17981.7009-0.19320.7486-11.6449-1.8938-5.4231
22.3177-0.03670.87021.73660.22732.0045-0.13270.3117-0.0785-0.12970.2373-0.0971-0.0460.1332-0.03790.1686-0.0786-0.04880.18010.02350.0472-46.687-13.762.333
31.32810.4096-0.08341.31520.28151.12040.0098-0.2547-0.03190.09420.1557-0.08370.04690.1277-0.06290.0774-0.006-0.03370.09450.04820.0817-51.2556-21.66419.7515
44.6892-1.61683.37712.485-1.14535.5066-0.37760.35340.65430.0190.0214-0.6526-0.7641.14460.22530.3626-0.0002-0.14530.449-0.18780.377-37.2529-0.622214.1738
53.86240.29863.71082.73020.58873.6060.1163-1.36090.07450.6645-0.0864-0.088-0.0591-0.31770.0030.297-0.1618-0.08921.0578-0.12840.4788-14.73255.2381-4.445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resid 1081 through 1106 ) or (resid 377 through 381 ))
2X-RAY DIFFRACTION2chain 'A' and (resid 382 through 456 )
3X-RAY DIFFRACTION3chain 'A' and (resid 17 through 195 )
4X-RAY DIFFRACTION4chain 'A' and ((resid 196 through 217) or (resid 1001 through 1002 ))
5X-RAY DIFFRACTION5chain 'A' and (resid 1003 through 1080 )

+
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