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- PDB-7tvi: Alpha1/BetaB Heteromeric Glycine Receptor in Glycine-Bound State -

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Basic information

Entry
Database: PDB / ID: 7tvi
TitleAlpha1/BetaB Heteromeric Glycine Receptor in Glycine-Bound State
Components
  • Glycine receptor beta subunit 2
  • Glycine receptor subunit alphaZ1
KeywordsMEMBRANE PROTEIN / Glycine / Ion Channel / Ligand-Gated / Receptor
Function / homology
Function and homology information


Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / transmitter-gated monoatomic ion channel activity / regulation of neuron differentiation / ligand-gated monoatomic ion channel activity / glycine binding / cellular response to zinc ion / cellular response to ethanol / chloride channel complex ...Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / transmitter-gated monoatomic ion channel activity / regulation of neuron differentiation / ligand-gated monoatomic ion channel activity / glycine binding / cellular response to zinc ion / cellular response to ethanol / chloride channel 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 / intracellular protein localization / perikaryon / postsynaptic membrane / dendrite / zinc ion binding / membrane / plasma membrane / cytoplasm
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 / Glycine receptor subunit alphaZ1 / Glycine receptor subunit beta
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGibbs, E. / Chakrapani, S. / Kumar, A.
Funding support United States, 1items
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, S.L. / Biggin, P.C. / Chakrapani, S.
History
DepositionFeb 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
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Revision 1.0Mar 22, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2May 14, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine receptor subunit alphaZ1
D: Glycine receptor subunit alphaZ1
C: Glycine receptor subunit alphaZ1
B: Glycine receptor subunit alphaZ1
E: Glycine receptor beta subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,67316
Polymers275,9715
Non-polymers1,70311
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Glycine receptor subunit alphaZ1


Mass: 52537.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: glra1
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: O93430
#2: Protein Glycine receptor beta subunit 2 / Glycine receptor / beta b


Mass: 65820.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: glrbb, glrb2
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q6DC22
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 6 / 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
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: .25 MDa / Experimental value: NO
Source (natural)Organism: Danio rerio (zebrafish)
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
220 mMHEPESC8H18N2O4S1
31 mMDodecyl-D-MaltopyranosideC24H46O111
41 mMGlycineC2H5NO21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Single Particle
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: FEI TITAN KRIOS / Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 700 nm / Specimen-ID: 1

ID
1
2
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1150GATAN K3 BIOQUANTUM (6k x 4k)
2240GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryImaging-IDDetails
2SerialEMimage acquisition1
4CTFFIND4.1CTF correction
8PHENIXmodel refinement
10EPUimage acquisition2
11cryoSPARC3.3.1initial Euler assignmentAb-initio
12cryoSPARC3.3.1final Euler assignmentNon-Uniform Refinement
13RELION4classification
14cryoSPARC3.3.13D reconstructionNon-Uniform Refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 350000
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205704 / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414089
ELECTRON MICROSCOPYf_angle_d0.78919119
ELECTRON MICROSCOPYf_dihedral_angle_d9.3061936
ELECTRON MICROSCOPYf_chiral_restr0.0512164
ELECTRON MICROSCOPYf_plane_restr0.0062384

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