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- PDB-8dn3: Cryo-EM structure of human Glycine Receptor alpha1-beta heteromer... -

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Basic information

Entry
Database: PDB / ID: 8dn3
TitleCryo-EM structure of human Glycine Receptor alpha1-beta heteromer, apo state
Components(Glycine receptor subunit ...) x 2
KeywordsMEMBRANE PROTEIN / glycine receptor subunit alpha-1 / glycine receptor subunit beta / Green fluorescent protein
Function / homology
Function and homology information


taurine binding / negative regulation of transmission of nerve impulse / synaptic transmission, glycinergic / positive regulation of acrosome reaction / acrosome reaction / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / gamma-aminobutyric acid receptor clustering / neuromuscular process controlling posture / postsynaptic specialization ...taurine binding / negative regulation of transmission of nerve impulse / synaptic transmission, glycinergic / positive regulation of acrosome reaction / acrosome reaction / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / gamma-aminobutyric acid receptor clustering / neuromuscular process controlling posture / postsynaptic specialization / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity / regulation of respiratory gaseous exchange by nervous system process / inhibitory synapse / glycinergic synapse / chloride transport / response to alcohol / adult walking behavior / inhibitory postsynaptic potential / glycine binding / cellular response to zinc ion / startle response / cellular response to ethanol / neuropeptide signaling pathway / chloride channel complex / neuronal action potential / monoatomic ion transport / visual perception / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / muscle contraction / chloride transmembrane transport / bioluminescence / generation of precursor metabolites and energy / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cellular response to amino acid stimulus / GABA-ergic synapse / transmembrane signaling receptor activity / nervous system development / perikaryon / chemical synaptic transmission / postsynaptic membrane / neuron projection / external side of plasma membrane / neuronal cell body / intracellular membrane-bounded organelle / dendrite / synapse / protein-containing complex binding / zinc ion binding / identical protein 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 ...: / 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 / Green fluorescent protein, GFP / 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-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
DECANE / nonane / HEXANE / HEPTANE / N-BUTANE / UNDECANE / Glycine receptor subunit beta / Glycine receptor subunit alpha-1 / Green fluorescent protein / Glycine receptor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsLiu, X. / Wang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R35GM146860 United States
CitationJournal: Nat Commun / Year: 2023
Title: Asymmetric gating of a human hetero-pentameric glycine receptor.
Authors: Xiaofen Liu / Weiwei Wang /
Abstract: Hetero-pentameric Cys-loop receptors constitute a major type of neurotransmitter receptors that enable signal transmission and processing in the nervous system. Despite intense investigations into ...Hetero-pentameric Cys-loop receptors constitute a major type of neurotransmitter receptors that enable signal transmission and processing in the nervous system. Despite intense investigations into their working mechanism and pharmaceutical potentials, how neurotransmitters activate these receptors remains unclear due to the lack of high-resolution structural information in the activated open state. Here we report near-atomic resolution structures resolved in digitonin consistent with all principle functional states of the human α1β GlyR, which is a major Cys-loop receptor that mediates inhibitory neurotransmission in the central nervous system of adults. Glycine binding induces cooperative and symmetric structural rearrangements in the neurotransmitter-binding extracellular domain but asymmetrical pore dilation in the transmembrane domain. Symmetric response in the extracellular domain is consistent with electrophysiological data showing cooperative glycine activation and contribution from both α1 and β subunits. A set of functionally essential but differentially charged amino acid residues in the transmembrane domain of the α1 and β subunits explains asymmetric activation. These findings provide a foundation for understanding how the gating of the Cys-loop receptor family members diverges to accommodate specific physiological environments.
History
DepositionJul 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 1, 2023Group: Database references / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity_name_com.entity_id / _entity_name_com.name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_seq_align_beg_ins_code / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Glycine receptor subunit alpha-1
A: Glycine receptor subunit alpha-1
B: Glycine receptor subunit alpha-1
C: Glycine receptor subunit alpha-1
E: Glycine receptor subunit beta,Green fluorescent protein,Glycine receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,51666
Polymers246,2695
Non-polymers7,24761
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Glycine receptor subunit ... , 2 types, 5 molecules DABCE

#1: Protein
Glycine receptor subunit alpha-1 / Glycine receptor 48 kDa subunit / Glycine receptor strychnine-binding subunit


Mass: 42421.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Derived by substitution of M3/M4 loop (residues R316-P381) s by GSSG peptide.
Source: (gene. exp.) Homo sapiens (human) / Gene: GLRA1 / Production host: Homo sapiens (human) / References: UniProt: P23415
#2: Protein Glycine receptor subunit beta,Green fluorescent protein,Glycine receptor beta


Mass: 76584.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aequorea victoria (jellyfish)
Gene: GLRB, GFP / Production host: Homo sapiens (human)
References: UniProt: P48167, UniProt: P42212, UniProt: A0A2K6CAQ3

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Sugars , 1 types, 5 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.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 7 types, 56 molecules

#4: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C6H14
#5: Chemical
ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C11H24
#6: Chemical
ChemComp-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C9H20
#7: Chemical
ChemComp-NBU / N-BUTANE


Mass: 58.122 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10
#8: Chemical
ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H16
#9: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: heteromeric glycine receptor alpha-1 and beta, apo state
Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.24 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Aequorea victoria (jellyfish)6100
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMsodium chlorideNaCl1
220 mMTris-HClTris-HCl1
30.06 % w/vdigitonindigitonin1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: 1000 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingElectron dose: 69.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29850 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 7MLY

7mly


Accession code: 7MLY / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE

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