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- PDB-9bzp: Homomeric alpha3 glycine receptor in the presence of 0.1 millimol... -

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Basic information

Entry
Database: PDB / ID: 9bzp
TitleHomomeric alpha3 glycine receptor in the presence of 0.1 millimolar glycine and 1 micromolar zinc in a desensitized state
ComponentsGlycine receptor subunit alpha-3
KeywordsMEMBRANE PROTEIN / Glycine / Ion Channel / Ligand-Gated / Pentameric
Function / homology
Function and homology information


glycine-gated chloride ion channel activity / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / neurotransmitter receptor activity / glycine binding / transmembrane transporter complex / chloride transmembrane transport / protein homooligomerization / transmembrane signaling receptor activity ...glycine-gated chloride ion channel activity / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / neurotransmitter receptor activity / glycine binding / transmembrane transporter complex / chloride transmembrane transport / protein homooligomerization / transmembrane signaling receptor activity / perikaryon / postsynaptic membrane / neuron projection / intracellular membrane-bounded organelle / dendrite / synapse / metal ion binding / plasma membrane
Similarity search - Function
Glycine receptor alpha3 / 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 ...Glycine receptor alpha3 / 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 / Chem-PIO / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Glycine receptor subunit alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsKindig, K. / Gibbs, E. / Chakrapani, S.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM131216 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134896 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3R01GM108921-03S1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108921-5S1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3R01GM131216-1S1 United States
National Institutes of Health/Office of the Director1S10OD032437 United States
CitationJournal: To Be Published
Title: Physiological modulation of alpha3 glycine receptors
Authors: Kindig, K. / Gibbs, E. / Chakrapani, S.
History
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine receptor subunit alpha-3
B: Glycine receptor subunit alpha-3
C: Glycine receptor subunit alpha-3
D: Glycine receptor subunit alpha-3
E: Glycine receptor subunit alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,97365
Polymers277,9055
Non-polymers35,06760
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein / Sugars , 2 types, 10 molecules ABCDE

#1: Protein
Glycine receptor subunit alpha-3


Mass: 55581.066 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLRA3
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: O75311
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 65 molecules

#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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: 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.: 25 / Source method: obtained synthetically / Formula: C25H49O19P3
#6: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: Pentameric Assembly of Human Glycine Receptor Subtype Alpha3
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: .25 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21478 / Symmetry type: POINT

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