[English] 日本語
Yorodumi
- PDB-3uu4: The GLIC pentameric Ligand-Gated Ion Channel Loop2-21' mutant red... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uu4
TitleThe GLIC pentameric Ligand-Gated Ion Channel Loop2-21' mutant reduced in the crystal in a locally-closed conformation (LC1 subtype)
ComponentsGlr4197 protein
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / Cys-loop receptor family
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / extracellular ligand-gated monoatomic ion 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
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsSauguet, L. / Nury, H. / Corringer, P.J. / Delarue, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: A locally closed conformation of a bacterial pentameric proton-gated ion channel.
Authors: Prevost, M.S. / Sauguet, L. / Nury, H. / Van Renterghem, C. / Huon, C. / Poitevin, F. / Baaden, M. / Delarue, M. / Corringer, P.J.
History
DepositionNov 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references
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: Glr4197 protein
B: Glr4197 protein
C: Glr4197 protein
D: Glr4197 protein
E: Glr4197 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,1366
Polymers182,6255
Non-polymers5111
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22150 Å2
ΔGint-144 kcal/mol
Surface area63090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.600, 133.890, 159.730
Angle α, β, γ (deg.)90.00, 102.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-319-

HOH

-
Components

#1: Protein
Glr4197 protein / GLIC / ligand-gated ion channel


Mass: 36524.977 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: C27S,K33C,N245C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#2: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 5.2 Å3/Da / Density % sol: 76.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 15% PEG4000, 0.4 M sodium thiocyanate, 0.1 M sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3.05→40.9 Å / Num. all: 71200 / Num. obs: 70985 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 90.4 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.043 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.7 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
3.05-3.210.5692.2103480.34699.7
3.05-40.90.0710.8709850.043100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EAM

3eam


Resolution: 3.05→27.28 Å / Cor.coef. Fo:Fc: 0.8574 / Cor.coef. Fo:Fc free: 0.8392 / SU R Cruickshank DPI: 0.531 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.473 / SU Rfree Blow DPI: 0.296 / SU Rfree Cruickshank DPI: 0.311
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 3556 5.01 %RANDOM
Rwork0.2207 ---
obs0.2218 70985 99.78 %-
Displacement parametersBiso mean: 104.69 Å2
Baniso -1Baniso -2Baniso -3
1--13.8721 Å20 Å246.8358 Å2
2---9.3754 Å20 Å2
3---23.2475 Å2
Refine analyzeLuzzati coordinate error obs: 0.71 Å
Refinement stepCycle: LAST / Resolution: 3.05→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12600 0 12 51 12663
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4284SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes255HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1870HARMONIC5
X-RAY DIFFRACTIONt_it12951HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1760SEMIHARMONIC5
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_contact14977SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12951HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg17705HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion18.91
LS refinement shellResolution: 3.05→3.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3241 254 4.85 %
Rwork0.284 4986 -
all0.2859 5240 -
obs--99.78 %

+
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