[English] 日本語
Yorodumi
- EMDB-23148: Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23148
TitleCyro-EM structure of human Glycine Receptor alpha2-beta heteromer, strychnine bound state, 3.8 Angstrom
Map data
Sample
  • Complex: Glycine receptor alpha2-beta heteromer with strychnine, 3.8 Angstrom
    • Organelle or cellular component: Glycine receptor subunit alpha-2
      • Protein or peptide: Glycine receptor subunit alpha-2
    • Organelle or cellular component: Glycine receptor subunit beta, Green fluorescent protein chimera
      • Protein or peptide: Glycine receptor subunit beta,Green fluorescent protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: STRYCHNINE
Keywordsglycine receptor / alpha2-beta hetero-pentamer / strychnine / MEMBRANE PROTEIN
Function / homology
Function and homology information


glycine-gated chloride ion channel activity / acrosome reaction / glycine-gated chloride channel complex / synaptic transmission, glycinergic / gamma-aminobutyric acid receptor clustering / Neurotransmitter receptors and postsynaptic signal transmission / postsynaptic specialization / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity ...glycine-gated chloride ion channel activity / acrosome reaction / glycine-gated chloride channel complex / synaptic transmission, glycinergic / gamma-aminobutyric acid receptor clustering / Neurotransmitter receptors and postsynaptic signal transmission / postsynaptic specialization / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity / glycinergic synapse / cellular response to ethanol / adult walking behavior / cellular response to zinc ion / neurotransmitter receptor activity / glycine binding / startle response / chloride channel complex / neuropeptide signaling pathway / transmembrane transporter complex / monoatomic ion transport / GABA-ergic synapse / chloride transmembrane transport / visual perception / bioluminescence / generation of precursor metabolites and energy / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cellular response to amino acid stimulus / transmembrane signaling receptor activity / nervous system development / monoatomic ion transmembrane transport / chemical synaptic transmission / postsynaptic membrane / neuron projection / intracellular membrane-bounded organelle / dendrite / synapse / protein-containing complex binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Glycine receptor alpha2 / : / Glycine receptor beta / : / Glycine receptor alpha / 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 ...Glycine receptor alpha2 / : / Glycine receptor beta / : / Glycine receptor alpha / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Glycine receptor subunit alpha-2 / Green fluorescent protein / Glycine receptor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYu H / Wang W
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationI-2020-20190330 United States
CitationJournal: Neuron / Year: 2021
Title: Characterization of the subunit composition and structure of adult human glycine receptors.
Authors: Hailong Yu / Xiao-Chen Bai / Weiwei Wang /
Abstract: The strychnine-sensitive pentameric glycine receptor (GlyR) mediates fast inhibitory neurotransmission in the mammalian nervous system. Only heteromeric GlyRs mediate synaptic transmission, as they ...The strychnine-sensitive pentameric glycine receptor (GlyR) mediates fast inhibitory neurotransmission in the mammalian nervous system. Only heteromeric GlyRs mediate synaptic transmission, as they contain the β subunit that permits clustering at the synapse through its interaction with scaffolding proteins. Here, we show that α2 and β subunits assemble with an unexpected 4:1 stoichiometry to produce GlyR with native electrophysiological properties. We determined structures in multiple functional states at 3.6-3.8 Å resolutions and show how 4:1 stoichiometry is consistent with the structural features of α2β GlyR. Furthermore, we show that one single β subunit in each GlyR gives rise to the characteristic electrophysiological properties of heteromeric GlyR, while more β subunits render GlyR non-conductive. A single β subunit ensures a univalent GlyR-scaffold linkage, which means the scaffold alone regulates the cluster properties.
History
DepositionDec 17, 2020-
Header (metadata) releaseSep 8, 2021-
Map releaseSep 8, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7l31
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23148.png

Downloads & links

-
Map

FileDownload / File: emd_23148.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0185 / Movie #1: 0.022
Minimum - Maximum-0.08879999 - 0.12468329
Average (Standard dev.)0.0008234038 (±0.005009226)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z212.480212.480212.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0890.1250.001

-
Supplemental data

-
Sample components

-
Entire : Glycine receptor alpha2-beta heteromer with strychnine, 3.8 Angstrom

EntireName: Glycine receptor alpha2-beta heteromer with strychnine, 3.8 Angstrom
Components
  • Complex: Glycine receptor alpha2-beta heteromer with strychnine, 3.8 Angstrom
    • Organelle or cellular component: Glycine receptor subunit alpha-2
      • Protein or peptide: Glycine receptor subunit alpha-2
    • Organelle or cellular component: Glycine receptor subunit beta, Green fluorescent protein chimera
      • Protein or peptide: Glycine receptor subunit beta,Green fluorescent protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: STRYCHNINE

-
Supramolecule #1: Glycine receptor alpha2-beta heteromer with strychnine, 3.8 Angstrom

SupramoleculeName: Glycine receptor alpha2-beta heteromer with strychnine, 3.8 Angstrom
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 257 KDa

-
Supramolecule #2: Glycine receptor subunit alpha-2

SupramoleculeName: Glycine receptor subunit alpha-2 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: Glycine receptor subunit beta, Green fluorescent protein chimera

SupramoleculeName: Glycine receptor subunit beta, Green fluorescent protein chimera
type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Glycine receptor subunit alpha-2

MacromoleculeName: Glycine receptor subunit alpha-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.676004 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KDHDSRSGKQ PSQTLSPSDF LDKLMGRTSG YDARIRPNFK GPPVNVTCNI FINSFGSVTE TTMDYRVNIF LRQQWNDSRL AYSEYPDDS LDLDPSMLDS IWKPDLFFAN EKGANFHDVT TDNKLLRISK NGKVLYSIRL TLTLSCPMDL KNFPMDVQTC T MQLESFGY ...String:
KDHDSRSGKQ PSQTLSPSDF LDKLMGRTSG YDARIRPNFK GPPVNVTCNI FINSFGSVTE TTMDYRVNIF LRQQWNDSRL AYSEYPDDS LDLDPSMLDS IWKPDLFFAN EKGANFHDVT TDNKLLRISK NGKVLYSIRL TLTLSCPMDL KNFPMDVQTC T MQLESFGY TMNDLIFEWL SDGPVQVAEG LTLPQFILKE EKELGYCTKH YNTGKFTCIE VKFHLERQMG YYLIQMYIPS LL IVILSWV SFWINMDAAP ARVALGITTV LTMTTQSSGS RASLPKVSYV KAIDIWMAVC LLFVFAALLE YAAVNFVSRG SSG KKFVDR AKRIDTISRA AFPLAFLIFN IFYWITYKII RHEDVHKK

UniProtKB: Glycine receptor subunit alpha-2, Glycine receptor subunit alpha-2

-
Macromolecule #2: Glycine receptor subunit beta,Green fluorescent protein

MacromoleculeName: Glycine receptor subunit beta,Green fluorescent protein
type: protein_or_peptide / ID: 2
Details: This is a GFP insertion between Glycine Receptor Beta M3-M4 helix
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 78.765086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GVAMPGAEDD VVAALEVLFQ GPKSSKKGKG KKKQYLCPSQ QSAEDLARVP ANSTSNILNR LLVSYDPRIR PNFKGIPVDV VVNIFINSF GSIQETTMDY RVNIFLRQKW NDPRLKLPSD FRGSDALTVD PTMYKCLWKP DLFFANEKSA NFHDVTQENI L LFIFRDGD ...String:
GVAMPGAEDD VVAALEVLFQ GPKSSKKGKG KKKQYLCPSQ QSAEDLARVP ANSTSNILNR LLVSYDPRIR PNFKGIPVDV VVNIFINSF GSIQETTMDY RVNIFLRQKW NDPRLKLPSD FRGSDALTVD PTMYKCLWKP DLFFANEKSA NFHDVTQENI L LFIFRDGD VLVSMRLSIT LSCPLDLTLF PMDTQRCKMQ LESFGYTTDD LRFIWQSGDP VQLEKIALPQ FDIKKEDIEY GN CTKYYKG TGYYTCVEVI FTLRRQVGFY MMGVYAPTLL IVVLSWLSFW INPDASAARV PLGIFSVLSL ASECTTLAAE LPK VSYVKA LDVWLIACLL FGFASLVEYA VVQVMLNGGS SAAAVSKGEE LFTGVVPILV ELDGDVNGHK FSVSGEGEGD ATYG KLTLK FICTTGKLPV PWPTLVTTLT YGVQCFSRYP DHMKQHDFFK SAMPEGYVQE RTIFFKDDGN YKTRAEVKFE GDTLV NRIE LKGIDFKEDG NILGHKLEYN YNSHNVYIMA DKQKNGIKVN FKIRHNIEDG SVQLADHYQQ NTPIGDGPVL LPDNHY LST QSKLSKDPNE KRDHMVLLEF VTAAGITLGM DELYKSGSGS GVGETRCKKV CTSKSDLRSN DFSIVGSLPR DFELSNY DC YGKPIEVNNG LGKSQAKNNK KPPPAKPVIP TAAKRIDLYA RALFPFCFLF FNVIYWSIYL

UniProtKB: Glycine receptor subunit beta, Green fluorescent protein, Glycine receptor subunit beta

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #4: STRYCHNINE

MacromoleculeName: STRYCHNINE / type: ligand / ID: 4 / Number of copies: 5 / Formula: SY9
Molecular weightTheoretical: 334.412 Da
Chemical component information

ChemComp-SY9:
STRYCHNINE / alkaloid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.5 mg/mL
BufferpH: 8 / Component:
ConcentrationFormula
20.0 mM
200.0 mMNaCl
1.0 mM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4111 / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.2 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 472972
Startup modelType of model: EMDB MAP
EMDB ID:

6346

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 38541
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 6 / Software - Name: RELION

-
Atomic model buiding 1

Initial modelPDB ID:

3jad


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-7l31:
Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, strychnine bound state, 3.8 Angstrom

+
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