[English] 日本語
Yorodumi
- PDB-8bn5: Crystal structure of the ligand-binding domain (LBD) of human iGl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bn5
TitleCrystal structure of the ligand-binding domain (LBD) of human iGluR Delta-1 (GluD1) in complex with GABA
ComponentsGlutamate receptor ionotropic, delta-1
KeywordsMEMBRANE PROTEIN / ion channel / ligand binding domain / glutamate receptor / GABA
Function / homology
Function and homology information


GABA receptor activity / trans-synaptic protein complex / negative regulation of synaptic plasticity / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / regulation of postsynapse organization / AMPA glutamate receptor activity / AMPA glutamate receptor complex / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels ...GABA receptor activity / trans-synaptic protein complex / negative regulation of synaptic plasticity / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / regulation of postsynapse organization / AMPA glutamate receptor activity / AMPA glutamate receptor complex / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / GABA-ergic synapse / phospholipase C-activating G protein-coupled receptor signaling pathway / dendritic spine / postsynaptic membrane / glutamatergic synapse / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
GAMMA-AMINO-BUTANOIC ACID / Glutamate receptor ionotropic, delta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHeroven, C. / Malinauskas, T. / Aricescu, A.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L009609/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/15 United Kingdom
CitationJournal: Science / Year: 2023
Title: GluD1 binds GABA and controls inhibitory plasticity.
Authors: Piot, L. / Heroven, C. / Bossi, S. / Zamith, J. / Malinauskas, T. / Johnson, C. / Wennagel, D. / Stroebel, D. / Charrier, C. / Aricescu, A.R. / Mony, L. / Paoletti, P.
History
DepositionNov 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor ionotropic, delta-1
B: Glutamate receptor ionotropic, delta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,50013
Polymers62,6952
Non-polymers80511
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-41 kcal/mol
Surface area25360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.838, 66.967, 175.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Glutamate receptor ionotropic, delta-1 / GluD1 / GluR delta-1 subunit


Mass: 31347.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRID1, KIAA1220 / Plasmid: pHR-CMV-TetO2 / Details (production host): transient transfection / Cell (production host): epithelial-like / Cell line (production host): HEK293S GnTI-/- / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): kidney; embryo / References: UniProt: Q9ULK0
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 5 types, 235 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% (w/v) PEG 4000, 100 mM HEPES pH 7.5, 200 mM CaCl2
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→87.71 Å / Num. obs: 37143 / % possible obs: 93.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 35.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.6 / Net I/σ(I): 10.3
Reflection shellResolution: 1.9→2.03 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.719 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1837 / CC1/2: 0.525 / Rpim(I) all: 0.6 / % possible all: 51.5

-
Processing

Software
NameVersionClassification
autoPROC1.0.5 (20210420)data processing
XDSFeb 5, 2021 (BUILT 20210205)data reduction
PHASER2.8.3phasing
REFMAC5.8.0270refinement
PHENIX1.20.1-4487refinement
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V3U

2v3u


Resolution: 1.9→44.35 Å / SU ML: 0.2265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2351
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2282 1809 4.87 %
Rwork0.1839 35331 -
obs0.186 37140 85.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4187 0 45 225 4457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434380
X-RAY DIFFRACTIONf_angle_d0.67855932
X-RAY DIFFRACTIONf_chiral_restr0.0473655
X-RAY DIFFRACTIONf_plane_restr0.0059762
X-RAY DIFFRACTIONf_dihedral_angle_d12.38831637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.345140.283156X-RAY DIFFRACTION4.9
1.95-2.010.2893550.28121020X-RAY DIFFRACTION32.66
2.01-2.070.3061990.24682367X-RAY DIFFRACTION74.66
2.07-2.150.30251550.2262955X-RAY DIFFRACTION94.19
2.15-2.230.26321560.21673124X-RAY DIFFRACTION99.21
2.23-2.340.27121810.21613109X-RAY DIFFRACTION100
2.34-2.460.26741630.19283180X-RAY DIFFRACTION100
2.46-2.610.23811470.18773177X-RAY DIFFRACTION100
2.61-2.810.2221810.19133155X-RAY DIFFRACTION99.91
2.81-3.10.26021680.20153188X-RAY DIFFRACTION100
3.1-3.550.23151630.17393246X-RAY DIFFRACTION100
3.55-4.470.18351660.15383229X-RAY DIFFRACTION99.97
4.47-44.350.2171710.17983425X-RAY DIFFRACTION99.94
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)
12.17098890518-0.4237756468160.9210356034911.93835240355-1.164570649553.790159001710.01352566544240.132378928518-0.177988050035-0.197481607423-0.07161073796450.177653257270.4431511266560.1355706039180.05105433886220.2468132551650.02770477896770.03559292234090.153531185805-0.006269897328970.31038603188921.271516150260.001891308114.1022925811
21.93570231043-0.155644434303-0.1397358506113.45204516755-1.065662848121.78513586878-0.103614111101-0.1362346512230.1285963513760.5263789646520.07627918144420.0518123495364-0.223045302997-0.07441892373090.05123688497870.3076019592540.04141441266320.06126634920190.258928716737-0.05649852171190.2466900682917.69110851185.108630731128.3289419284
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 437 through 815)AA437 - 8142 - 265
22(chain 'B' and resid 437 through 816)BB437 - 8161 - 266

+
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