[English] 日本語
Yorodumi
- EMDB-6998: Cryo-EM structure of the human alpha5beta3 GABAA receptor in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6998
TitleCryo-EM structure of the human alpha5beta3 GABAA receptor in complex with GABA and Nb25
Map dataCryoEM Structure of the human %u03B15%u03B23 GABAA receptor
Sample
  • Complex: Pentameric complex of 1 alpha and 4 beta GABA receptor
    • Protein or peptide: Nb25
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
KeywordsIRON CHANNEL / MEMBRANE PROTEIN
Function / homology
Function and homology information


inhibitory extracellular ligand-gated monoatomic ion channel activity / benzodiazepine receptor activity / cellular response to histamine / GABA receptor activation / inner ear receptor cell development / GABA-gated chloride ion channel activity / GABA-A receptor activity / GABA-A receptor complex / GABA receptor binding / inhibitory synapse assembly ...inhibitory extracellular ligand-gated monoatomic ion channel activity / benzodiazepine receptor activity / cellular response to histamine / GABA receptor activation / inner ear receptor cell development / GABA-gated chloride ion channel activity / GABA-A receptor activity / GABA-A receptor complex / GABA receptor binding / inhibitory synapse assembly / innervation / synaptic transmission, GABAergic / postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / nervous system process / neurotransmitter receptor activity / cochlea development / neuronal cell body membrane / roof of mouth development / Signaling by ERBB4 / associative learning / chloride channel complex / GABA-ergic synapse / transmembrane transporter complex / behavioral fear response / regulation of postsynaptic membrane potential / chloride transmembrane transport / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / cytoplasmic vesicle membrane / presynaptic membrane / signaling receptor activity / postsynapse / postsynaptic membrane / neuron projection / synapse / signal transduction / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 5 subunit / Gamma-aminobutyric-acid A receptor, beta subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily ...Gamma-aminobutyric-acid A receptor, alpha 5 subunit / Gamma-aminobutyric-acid A receptor, beta subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / 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
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor subunit beta-3 / Gamma-aminobutyric acid receptor subunit alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsLiu S / Xu L
Funding support China, United States, 13 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500404 China
Ministry of Science and Technology (China)2014CB910300 China
Ministry of Science and Technology (China)2016YFA0501102 China
National Natural Science Foundation of China31630030 China
National Natural Science Foundation of China31525001 China
National Natural Science Foundation of China31430019 China
National Natural Science Foundation of China31600606 China
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM071940 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10RR23057 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10OD018111 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)U24GM116792 United States
National Science Foundation (China)DBI-1338135 China
National Science Foundation (China)DMR-1548924 China
CitationJournal: Cell Res / Year: 2018
Title: Cryo-EM structure of the human α5β3 GABA receptor.
Authors: Si Liu / Lingyi Xu / Fenghui Guan / Yun-Tao Liu / Yanxiang Cui / Qing Zhang / Xiang Zheng / Guo-Qiang Bi / Z Hong Zhou / Xiaokang Zhang / Sheng Ye /
History
DepositionJul 11, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseOct 3, 2018-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6a96
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6998.png

Downloads & links

-
Map

FileDownload / File: emd_6998.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM Structure of the human %u03B15%u03B23 GABAA receptor
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 7.0 / Movie #1: 7
Minimum - Maximum-12.891079 - 22.949110000000001
Average (Standard dev.)-0.023008518 (±0.8374582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.920273.920273.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-12.89122.949-0.023

-
Supplemental data

-
Sample components

-
Entire : Pentameric complex of 1 alpha and 4 beta GABA receptor

EntireName: Pentameric complex of 1 alpha and 4 beta GABA receptor
Components
  • Complex: Pentameric complex of 1 alpha and 4 beta GABA receptor
    • Protein or peptide: Nb25
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5
  • Ligand: GAMMA-AMINO-BUTANOIC ACID

-
Supramolecule #1: Pentameric complex of 1 alpha and 4 beta GABA receptor

SupramoleculeName: Pentameric complex of 1 alpha and 4 beta GABA receptor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Nb25

MacromoleculeName: Nb25 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.673024 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCAASGHTFN YPIMGWFRQA PGKEREFVGA ISWSGGSTSY ADSVKDRFTI SRDNAKNTVY LEMNNLKPE DTAVYYCAAK GRYSGGLYYP TNYDYWGQGT QVTVSS

-
Macromolecule #2: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyri...

MacromoleculeName: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.052711 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWGLAGGRLF GIFSAPVLVA VVCCAQSVND PGNMSFVKET VDKLLKGYDI RLRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQ QYWRDKRLAY SGIPLNLTLD NRVADQLWVP DTYFLNDKKS FVHGVTVKNR MIRLHPDGTV LYGLRITTTA A CMMDLRRY ...String:
MWGLAGGRLF GIFSAPVLVA VVCCAQSVND PGNMSFVKET VDKLLKGYDI RLRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQ QYWRDKRLAY SGIPLNLTLD NRVADQLWVP DTYFLNDKKS FVHGVTVKNR MIRLHPDGTV LYGLRITTTA A CMMDLRRY PLDEQNCTLE IESYGYTTDD IEFYWRGGDK AVTGVERIEL PQFSIVEHRL VSRNVVFATG AYPRLSLSFR LK RNIGYFI LQTYMPSILI TILSWVSFWI NYDASAARVA LGITTVLTMT TINTHLRETL PKIPYVKAID MYLMGCFVFV FLA LLEYAF VNYIFFSQPA RAAAIDRWSR IVFPFTFSLF NLVYWLYYVN

UniProtKB: Gamma-aminobutyric acid receptor subunit beta-3, Gamma-aminobutyric acid receptor subunit beta-3

-
Macromolecule #3: Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyr...

MacromoleculeName: Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.456113 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDNGMFSGFI MIKNLLLFCI SMNLSSHFGF SQMPTSSVKD ETNDNITIFT RILDGLLDGY DNRLRPGLGE RITQVRTDIY VTSFGPVSD TEMEYTIDVF FRQSWKDERL RFKGPMQRLP LNNLLASKIW TPDTFFHNGK KSIAHNMTTP NKLLRLEDDG T LLYTMRLT ...String:
MDNGMFSGFI MIKNLLLFCI SMNLSSHFGF SQMPTSSVKD ETNDNITIFT RILDGLLDGY DNRLRPGLGE RITQVRTDIY VTSFGPVSD TEMEYTIDVF FRQSWKDERL RFKGPMQRLP LNNLLASKIW TPDTFFHNGK KSIAHNMTTP NKLLRLEDDG T LLYTMRLT ISAECPMQLE DFPMDAHACP LKFGSYAYPN SEVVYVWTNG STKSVVVAED GSRLNQYHLM GQTVGTENIS TS TGEYTIM TAHFHLKRKI GYFVIQTYLP CIMTVILSQV SFWLNRESVP ARTVFGVTTV LTMTTLSISA RNSLPKVAYA TAM DWFIAV CYAFVFSALI EFATVNYFTK SQPARAAKID KMSRIVFPVL FGTFNLVYWA TYLNREPVIK GAASPK

UniProtKB: Gamma-aminobutyric acid receptor subunit alpha-5, Gamma-aminobutyric acid receptor subunit alpha-5

-
Macromolecule #8: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 8 / Number of copies: 1 / Formula: ABU
Molecular weightTheoretical: 103.12 Da
Chemical component information

ChemComp-ABU:
GAMMA-AMINO-BUTANOIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 8.0 sec. / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.55) / Number images used: 161455
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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://pdbjlvh1.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