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- EMDB-26141: Alpha1/BetaB Heteromeric Glycine Receptor in Glycine-Bound State -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-26141
TitleAlpha1/BetaB Heteromeric Glycine Receptor in Glycine-Bound State
Map data
Sample
  • Complex: Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor
    • Protein or peptide: Glycine receptor subunit alphaZ1
    • Protein or peptide: Glycine receptor beta subunit 2
  • Ligand: GLYCINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGlycine / Ion Channel / Ligand-Gated / Receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


synaptic transmission, glycinergic / transmitter-gated monoatomic ion channel activity / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / cellular response to ethanol / cellular response to zinc ion / regulation of neuron differentiation / neurotransmitter receptor activity / glycine binding ...synaptic transmission, glycinergic / transmitter-gated monoatomic ion channel activity / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / cellular response to ethanol / cellular response to zinc ion / regulation of neuron differentiation / neurotransmitter receptor activity / glycine binding / chloride channel complex / ligand-gated monoatomic ion channel activity / transmembrane transporter complex / response to amino acid / monoatomic ion transport / chloride transmembrane transport / central nervous system development / cellular response to amino acid stimulus / transmembrane signaling receptor activity / protein localization / perikaryon / postsynaptic membrane / neuron projection / dendrite / synapse / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Glycine receptor beta / : / Glycine receptor alpha1 / 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 ...Glycine receptor beta / : / Glycine receptor alpha1 / 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
Similarity search - Domain/homology
Glycine receptor subunit alphaZ1 / Glycine receptor beta subunit 2
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGibbs E / Chakrapani S / Kumar A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM134896 United States
CitationJournal: Nat Commun / Year: 2023
Title: Conformational transitions and allosteric modulation in a heteromeric glycine receptor
Authors: Gibbs E / Klemm E / Seiferth D / Kumar A / Ilca SL / Biggin PC / Chakrapani S
History
DepositionFeb 4, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26141.png

Downloads & links

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Map

FileDownload / File: emd_26141.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-1.1413952 - 2.3041768
Average (Standard dev.)0.0010292883 (±0.045119643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26141_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26141_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26141_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor

EntireName: Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor
Components
  • Complex: Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor
    • Protein or peptide: Glycine receptor subunit alphaZ1
    • Protein or peptide: Glycine receptor beta subunit 2
  • Ligand: GLYCINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor

SupramoleculeName: Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Glycine receptor subunit alphaZ1

MacromoleculeName: Glycine receptor subunit alphaZ1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 52.537598 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MFALGIYLWE TIVFFSLAAS QQAAARKAAS PMPPSEFLDK LMGKVSGYDA RIRPNFKGPP VNVTCNIFIN SFGSIAETTM DYRVNIFLR QQWNDPRLAY SEYPDDSLDL DPSMLDSIWK PDLFFANEKG ANFHEVTTDN KLLRISKNGN VLYSIRITLV L ACPMDLKN ...String:
MFALGIYLWE TIVFFSLAAS QQAAARKAAS PMPPSEFLDK LMGKVSGYDA RIRPNFKGPP VNVTCNIFIN SFGSIAETTM DYRVNIFLR QQWNDPRLAY SEYPDDSLDL DPSMLDSIWK PDLFFANEKG ANFHEVTTDN KLLRISKNGN VLYSIRITLV L ACPMDLKN FPMDVQTCIM QLESFGYTMN DLIFEWDEKG AVQVADGLTL PQFILKEEKD LRYCTKHYNT GKFTCIEARF HL ERQMGYY LIQMYIPSLL IVILSWVSFW INMDAAPARV GLGITTVLTM TTQSSGSRAS LPKVSYVKAI DIWMAVCLLF VFS ALLEYA AVNFIARQHK ELLRFQRRRR HLKEDEAGDG RFSFAAYGMG PACLQAKDGM AIKGNNNNAP TSTNPPEKTV EEMR KLFIS RAKRIDTVSR VAFPLVFLIF NIFYWITYKI IRSEDIHKQL VPRGSHHHHH HHH

UniProtKB: Glycine receptor subunit alphaZ1

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Macromolecule #2: Glycine receptor beta subunit 2

MacromoleculeName: Glycine receptor beta subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 65.820281 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MKALKVIFML LIICLWMEGG FTKEKSAKKW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGS WSHPQFEKEN LYFQGEKSAK KGKKKGKQVY CPSQLSSEDL ARVPANSTSN ILNKLLITYD PRIRPNFKGI P VEDRVNIF ...String:
MKALKVIFML LIICLWMEGG FTKEKSAKKW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGS WSHPQFEKEN LYFQGEKSAK KGKKKGKQVY CPSQLSSEDL ARVPANSTSN ILNKLLITYD PRIRPNFKGI P VEDRVNIF INSFGSIQET TMDYRVNIFL RQRWNDPRLR LPQDFKSDSL TVDPKMFKCL WKPDLFFANE KSANFHDVTQ EN ILLFIFR NGDVLISMRL SVTLSCPLDL TLFPMDTQRC KMQLESFGYT TDDLQFMWQS GDPVQMDEIA LPQFDIKQED IEY GNCTKY YAGTGYYTCV EVIFTLRRQV GFYMMGVYAP TLLIVVLSWL SFWINPDASA ARVPLGILSV LSLSSECTSL ASEL PKVSY VKAIDIWLIA CLLFGFASLV EYAVVQVMLN SPKLLEAERA KIATKEKAEG KTPAKNTING MGSTPIHVST LQVTE TRCK KVCTSKSDLR TNDFSIVGSL PRDFELSNFD CYGKPIEVGS AFSKSQAKNN KKPPPPKPVI PSAAKRIDLY ARALFP FSF LFFNVIYWSV YLENLYFQGT ETSQVAPA

UniProtKB: Glycine receptor beta subunit 2

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Macromolecule #3: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 3 / Number of copies: 5 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMC8H18N2O4SHEPES
1.0 mMC24H46O11Dodecyl-D-Maltopyranoside
1.0 mMC2H5NO2Glycine
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsSingle Particle

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Particle selectionNumber selected: 350000
Startup modelType of model: OTHER / Details: AlphaFold
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: Non-Uniform Refinement / Number images used: 205704
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: Ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) / Software - details: Non-Uniform Refinement
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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