[English] 日本語
Yorodumi
- PDB-5mur: X-ray structure of the F14'A mutant of GLIC in complex with propofol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mur
TitleX-ray structure of the F14'A mutant of GLIC in complex with propofol
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane signaling receptor activity / identical protein binding / plasma membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / 2,6-BIS(1-METHYLETHYL)PHENOL / DIUNDECYL PHOSPHATIDYL CHOLINE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSauguet, L. / Fourati, Z. / Delarue, M.
CitationJournal: Cell Rep / Year: 2018
Title: Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels.
Authors: Fourati, Z. / Howard, R.J. / Heusser, S.A. / Hu, H. / Ruza, R.R. / Sauguet, L. / Lindahl, E. / Delarue, M.
History
DepositionJan 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proton-gated ion channel
B: Proton-gated ion channel
C: Proton-gated ion channel
D: Proton-gated ion channel
E: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,38433
Polymers181,0085
Non-polymers4,37628
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30270 Å2
ΔGint-260 kcal/mol
Surface area62660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.281, 132.972, 158.976
Angle α, β, γ (deg.)90.00, 102.10, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Proton-gated ion channel / GLIC / Ligand-gated ion channel / LGIC


Mass: 36201.625 Da / Num. of mol.: 5 / Fragment: UNP residues 43-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria)
Gene: glvI, glr4197 / Production host: Gloeobacter (bacteria) / References: UniProt: Q7NDN8

-
Non-polymers , 6 types, 150 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#6: Chemical ChemComp-PFL / 2,6-BIS(1-METHYLETHYL)PHENOL / 2,6-DIISOPROPYLPHENOL / PROPOFOL / Propofol


Mass: 178.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.15 Å3/Da / Density % sol: 76.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Na acetate pH4 12-15% PEG4K 200 mM NaSCN 16% glycerol 2% DMSO

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.1→49 Å / Num. obs: 66286 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 94.16 Å2 / Net I/σ(I): 16.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HFB

4hfb


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.9175 / Cor.coef. Fo:Fc free: 0.9159 / SU R Cruickshank DPI: 0.599 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.525 / SU Rfree Blow DPI: 0.272 / SU Rfree Cruickshank DPI: 0.284
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 3286 5.05 %RANDOM
Rwork0.1939 ---
obs0.1944 65133 97.73 %-
Displacement parametersBiso mean: 101.8 Å2
Baniso -1Baniso -2Baniso -3
1--10.9207 Å20 Å226.7136 Å2
2---5.2597 Å20 Å2
3---16.1804 Å2
Refine analyzeLuzzati coordinate error obs: 0.439 Å
Refinement stepCycle: 1 / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12610 0 247 122 12979
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00713168HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9217976HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4420SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes261HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1912HARMONIC5
X-RAY DIFFRACTIONt_it13168HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion19.48
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1767SEMIHARMONIC5
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_contact14975SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 215 4.48 %
Rwork0.2624 4583 -
all0.2633 4798 -
obs--97.85 %
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)
11.6747-0.09991.27730.6698-0.06463.2141-0.0435-0.10760.1752-0.00210.04440.0454-0.5008-0.3376-0.00080.11540.1196-0.1199-0.2399-0.0208-0.195539.5141-6.471729.7837
22.57060.31313.07160.52140.5345.29120.1024-0.1736-0.09820.1499-0.01890.11490.0377-0.3561-0.0835-0.16790.0416-0.0588-0.01010.0167-0.16127.7099-28.051935.7507
31.43630.37151.8110.98140.50484.40280.16980.0095-0.2988-0.0265-0.00240.10980.31040.0751-0.1674-0.03830.0848-0.1923-0.2324-0.0515-0.074541.9976-47.55428.514
41.30450.04911.50490.82770.05344.93860.00730.1946-0.1488-0.14830.0229-0.1766-0.07880.3938-0.0302-0.09080.1143-0.0927-0.1407-0.1016-0.14563.0049-38.06517.6012
51.4226-0.35311.84910.8909-0.9565.0507-0.07290.0420.1541-0.14720.018-0.1652-0.21030.1340.05490.0216-0.0722-0.0666-0.2150.0181-0.170361.4549-12.717318.6319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

+
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