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- PDB-3jae: Structure of alpha-1 glycine receptor by single particle electron... -

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Basic information

Entry
Database: PDB / ID: 3jae
TitleStructure of alpha-1 glycine receptor by single particle electron cryo-microscopy, glycine-bound state
ComponentsGlycine receptor subunit alphaZ1
KeywordsSIGNALING PROTEIN / cys loop receptor / alpha-1 glycine receptor / glycine
Function / homology
Function and homology information


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 ...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 / perikaryon / postsynaptic membrane / neuron projection / dendrite / synapse / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Glycine receptor alpha1 / Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 alpha1 / Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Glycine receptor subunit alphaZ1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsDu, J. / Lu, W. / Wu, S.P. / Cheng, Y.F. / Gouaux, E.
CitationJournal: Nature / Year: 2015
Title: Glycine receptor mechanism elucidated by electron cryo-microscopy.
Authors: Juan Du / Wei Lü / Shenping Wu / Yifan Cheng / Eric Gouaux /
Abstract: The strychnine-sensitive glycine receptor (GlyR) mediates inhibitory synaptic transmission in the spinal cord and brainstem and is linked to neurological disorders, including autism and hyperekplexia. ...The strychnine-sensitive glycine receptor (GlyR) mediates inhibitory synaptic transmission in the spinal cord and brainstem and is linked to neurological disorders, including autism and hyperekplexia. Understanding of molecular mechanisms and pharmacology of glycine receptors has been hindered by a lack of high-resolution structures. Here we report electron cryo-microscopy structures of the zebrafish α1 GlyR with strychnine, glycine, or glycine and ivermectin (glycine/ivermectin). Strychnine arrests the receptor in an antagonist-bound closed ion channel state, glycine stabilizes the receptor in an agonist-bound open channel state, and the glycine/ivermectin complex adopts a potentially desensitized or partially open state. Relative to the glycine-bound state, strychnine expands the agonist-binding pocket via outward movement of the C loop, promotes rearrangement of the extracellular and transmembrane domain 'wrist' interface, and leads to rotation of the transmembrane domain towards the pore axis, occluding the ion conduction pathway. These structures illuminate the GlyR mechanism and define a rubric to interpret structures of Cys-loop receptors.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)198,24010
Polymers196,1185
Non-polymers2,1225
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid A
31chain C and segid A
41chain D and segid A
51chain E and segid A

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid AB0
311chain C and segid AC0
411chain D and segid AD0
511chain E and segid AE0

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Components

#1: Protein
Glycine receptor subunit alphaZ1 / alpha1 glycine receptor


Mass: 39223.539 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: glra1 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O93430*PLUS
#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
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: zebra fish alpha-1 glycine receptor bound with glycine
Type: COMPLEX / Details: pentamer
Molecular weightValue: 0.2 MDa / Experimental value: NO
Buffer solutionName: 150 mM NaCl, 20 mM Tris-HCl, 1 mM C12M, 10 mM glycine / pH: 8
Details: 150 mM NaCl, 20 mM Tris-HCl, 1 mM C12M, 10 mM glycine
SpecimenConc.: 3.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 200 mesh copper 1.2/1.3 Quantifoil carbon grid
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temp: 90 K / Humidity: 100 %
Details: Blot for 3.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).
Method: Blot for 3.5 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Dec 8, 2014
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: -1500 nm / Cs: 2 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 1460
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2RELION3D reconstruction
CTF correctionDetails: each particle
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58188 / Nominal pixel size: 1.2156 Å / Actual pixel size: 1.2156 Å
Details: Particle picking, 2D classification, 3D classification, refinement, and reconstruction were done using Relion. Movies were aligned using motioncorr. (Single particle--Applied symmetry: C5)
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: REFINEMENT PROTOCOL--rigid body DETAILS--The model (3RHW) was fit into the density map using UCSF Chimera. Further de novo model building was done using COOT.
Atomic model building

3D fitting-ID: 1 / Accession code: 3RHW / Initial refinement model-ID: 1 / PDB-ID: 3RHW

3rhw

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1A
2B
3C
4D
5E
RefinementResolution: 3.9→49.314 Å / SU ML: 0.97 / σ(F): 10 / Phase error: 39.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.351 43762 5 %
Rwork0.3458 832039 -
obs0.3461 875801 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.39 Å2 / Biso mean: 102.788 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.9→49.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12685 0 140 0 12825
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00613155
ELECTRON MICROSCOPYf_angle_d1.11418000
ELECTRON MICROSCOPYf_chiral_restr0.0452130
ELECTRON MICROSCOPYf_plane_restr0.0062245
ELECTRON MICROSCOPYf_dihedral_angle_d9.7434430
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7575ELECTRON MICROSCOPY0.511TORSIONAL
12B7575ELECTRON MICROSCOPY0.511TORSIONAL
13C7575ELECTRON MICROSCOPY0.511TORSIONAL
14D7575ELECTRON MICROSCOPY0.511TORSIONAL
15E7575ELECTRON MICROSCOPY0.511TORSIONAL
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9003-3.94460.799114240.80892807929503100
3.9446-3.9910.566814660.57692778429250100
3.991-4.03970.522214880.51922770329191100
4.0397-4.09080.495914620.49592744328905100
4.0908-4.14460.474814860.46442780729293100
4.1446-4.20130.47915120.45852769929211100
4.2013-4.26130.443914680.45672801729485100
4.2613-4.32490.40814480.42072741328861100
4.3249-4.39240.385614610.39572769629157100
4.3924-4.46440.386114560.3832779529251100
4.4644-4.54130.38115000.38212793329433100
4.5413-4.62380.367814010.36232762829029100
4.6238-4.71270.33715500.33252787829428100
4.7127-4.80880.344714980.32362793529433100
4.8088-4.91330.32614170.32442766029077100
4.9133-5.02750.335914330.32882766229095100
5.0275-5.15310.32314450.33152783929284100
5.1531-5.29230.323914550.31842777229227100
5.2923-5.44780.361314590.35112760929068100
5.4478-5.62340.37214710.36372781329284100
5.6234-5.82410.347614430.34132767029113100
5.8241-6.05690.362414320.35142791229344100
6.0569-6.3320.362414980.3592778029278100
6.332-6.66510.334614950.33022748628981100
6.6651-7.08150.328914090.3292784229251100
7.0815-7.62650.280514590.28852778329242100
7.6265-8.39060.274414520.27122780629258100
8.3906-9.59690.25714420.25582766429106100
9.5969-12.06180.198414030.1899274352883899
12.0618-49.31770.318114290.303274962892599

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