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- PDB-7tu9: Alpha1/BetaB Heteromeric Glycine Receptor in Strychnine-Bound State -

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Basic information

Entry
Database: PDB / ID: 7tu9
TitleAlpha1/BetaB Heteromeric Glycine Receptor in Strychnine-Bound State
Components(Glycine receptor ...) x 2
KeywordsMEMBRANE PROTEIN / Glycine / Ion Channel / Strychnine
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 / cellular response to ethanol / cellular response to zinc ion / regulation of neuron differentiation / ligand-gated monoatomic ion channel activity / glycine binding / response to amino acid ...Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / transmitter-gated monoatomic ion channel activity / cellular response to ethanol / cellular response to zinc ion / regulation of neuron differentiation / ligand-gated monoatomic ion channel activity / glycine binding / response to amino acid / chloride channel complex / 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
Similarity search - Function
Glycine receptor beta / : / Glycine receptor alpha1 / Glycine receptor alpha / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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 transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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
Chem-PIO / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / STRYCHNINE / Glycine receptor subunit alphaZ1 / Glycine receptor beta subunit 2
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsGibbs, E. / Kumar, A. / Chakrapani, S.
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 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: 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
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Revision 1.1Oct 23, 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)293,22536
Polymers275,9715
Non-polymers17,25431
Water00
1


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

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Components

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Glycine receptor ... , 2 types, 5 molecules ADCBE

#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

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Sugars , 1 types, 6 molecules

#3: 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

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Non-polymers , 3 types, 25 molecules

#4: Chemical
ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C25H49O19P3
#5: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#6: Chemical
ChemComp-SY9 / STRYCHNINE


Mass: 334.412 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H22N2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM

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Details

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: 0.25 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
4100 uMStrychnineC21H22N2O21
SpecimenConc.: 0.1 mg/ml / Embedding 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2Leginonimage acquisition
4CTFFIND4.1CTF correction
8PHENIXmodel refinement
10cryoSPARC3.3.1initial Euler assignmentAb-Initio
11cryoSPARC3.3.1final Euler assignmentNon-Uniform Refinment
12RELION4classification
13cryoSPARC3.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 200000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131757 / Details: Non-Uniform Refinement Cryosparc / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314643
ELECTRON MICROSCOPYf_angle_d0.62719844
ELECTRON MICROSCOPYf_dihedral_angle_d6.9682071
ELECTRON MICROSCOPYf_chiral_restr0.0472220
ELECTRON MICROSCOPYf_plane_restr0.0042447

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