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- EMDB-9403: Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer... -

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Basic information

Entry
Database: EMDB / ID: EMD-9403
TitleCyro-EM structure of human Glycine Receptor alpha2-beta heteromer, Glycine bound, desensitized state
Map data
Sample
  • Complex: Glycine receptor alpha2-beta heteromer, glycine bound, desensitized state
    • Complex: Glycine receptor alpha2
      • Protein or peptide: Glycine receptor subunit alpha-2
    • Complex: Glycine receptor beta, GFP chimera
      • Protein or peptide: Glycine receptor subunit beta,Green fluorescent protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLYCINE
Function / homology
Function and homology information


glycine-gated chloride ion channel activity / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / acrosome reaction / gamma-aminobutyric acid receptor clustering / postsynaptic specialization / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity / synaptic transmission, glycinergic ...glycine-gated chloride ion channel activity / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / acrosome reaction / gamma-aminobutyric acid receptor clustering / postsynaptic specialization / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity / synaptic transmission, glycinergic / glycinergic synapse / cellular response to ethanol / adult walking behavior / cellular response to zinc ion / glycine binding / startle response / chloride channel complex / neuropeptide signaling pathway / GABA-ergic synapse / response to amino acid / monoatomic ion transport / chloride transmembrane transport / visual perception / monoatomic ion transmembrane transport / bioluminescence / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / generation of precursor metabolites and energy / cellular response to amino acid stimulus / transmembrane signaling receptor activity / nervous system development / 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: 3.6 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
DepositionMar 19, 2021-
Header (metadata) releaseSep 8, 2021-
Map releaseSep 8, 2021-
UpdateSep 8, 2021-
Current statusSep 8, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5bkf
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9403.png

Downloads & links

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Map

FileDownload / File: emd_9403.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.02
Minimum - Maximum-0.09061422 - 0.113021486
Average (Standard dev.)0.0004792036 (±0.0047475314)
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/NZ-40-113-15
NX/NY/NZ10616274
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0910.1130.000

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Supplemental data

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Sample components

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Entire : Glycine receptor alpha2-beta heteromer, glycine bound, desensitiz...

EntireName: Glycine receptor alpha2-beta heteromer, glycine bound, desensitized state
Components
  • Complex: Glycine receptor alpha2-beta heteromer, glycine bound, desensitized state
    • Complex: Glycine receptor alpha2
      • Protein or peptide: Glycine receptor subunit alpha-2
    • Complex: Glycine receptor beta, GFP chimera
      • Protein or peptide: Glycine receptor subunit beta,Green fluorescent protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLYCINE

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Supramolecule #1: Glycine receptor alpha2-beta heteromer, glycine bound, desensitiz...

SupramoleculeName: Glycine receptor alpha2-beta heteromer, glycine bound, desensitized state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightExperimental: 257 KDa

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Supramolecule #2: Glycine receptor alpha2

SupramoleculeName: Glycine receptor alpha2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: Glycine receptor beta, GFP chimera

SupramoleculeName: Glycine receptor beta, GFP chimera / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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

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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 helices M3-M4 of Glycine Receptor Beta
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

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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 / N-Acetylglucosamine

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Macromolecule #4: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 4 / Number of copies: 5 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE / Glycine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5.0 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris
200.0 mMSodium chlorideNaClSodium chloride
2.0 mMGlycine
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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 FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5999 / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 555287
CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

6346

Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final 3D classificationNumber classes: 6 / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 56419

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Atomic model buiding 1

Initial modelPDB ID:

7kuy

RefinementSpace: REAL
Output model

PDB-5bkf:
Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, Glycine bound, desensitized state

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