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- PDB-7mly: Cryo-EM reveals partially and fully assembled native glycine rece... -

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Basic information

Entry
Database: PDB / ID: 7mly
TitleCryo-EM reveals partially and fully assembled native glycine receptors,heteromeric pentamer
Components
  • (Glycine receptor ...) x 2
  • 3D1 Fab Heavy Chain
  • 3D1 Fab Light Chain
KeywordsMEMBRANE PROTEIN / SIGNALING PROTEIN / glycine receptor / ion channel / heteromeric pentamer
Function / homology
Function and homology information


Neurotransmitter receptors and postsynaptic signal transmission / taurine binding / glycine-gated chloride channel complex / negative regulation of transmission of nerve impulse / positive regulation of acrosome reaction / acrosome reaction / gamma-aminobutyric acid receptor clustering / neuromuscular process controlling posture / inhibitory synapse / extracellularly glycine-gated ion channel activity ...Neurotransmitter receptors and postsynaptic signal transmission / taurine binding / glycine-gated chloride channel complex / negative regulation of transmission of nerve impulse / positive regulation of acrosome reaction / acrosome reaction / gamma-aminobutyric acid receptor clustering / neuromuscular process controlling posture / inhibitory synapse / extracellularly glycine-gated ion channel activity / righting reflex / regulation of respiratory gaseous exchange by nervous system process / extracellularly glycine-gated chloride channel activity / synaptic transmission, glycinergic / glycinergic synapse / inhibitory postsynaptic potential / cellular response to ethanol / adult walking behavior / nervous system process / cellular response to zinc ion / neurotransmitter receptor activity / glycine binding / startle response / plasma membrane => GO:0005886 / chloride channel complex / GABA-ergic synapse / neuronal action potential / neuropeptide signaling pathway / response to amino acid / monoatomic ion transport / monoatomic ion transmembrane transport / chloride transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / visual perception / muscle contraction / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / cellular response to amino acid stimulus / transmembrane signaling receptor activity / nervous system development / chemical synaptic transmission / postsynaptic membrane / perikaryon / neuron projection / external side of plasma membrane / intracellular membrane-bounded organelle / synapse / dendrite / signal transduction / zinc ion binding
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 / Neuronal acetylcholine receptor ...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
DECANE / DODECANE / nonane / GLYCINE / HEXANE / HEPTANE / PENTANE / PENTADECANE / N-BUTANE / N-OCTANE ...DECANE / DODECANE / nonane / GLYCINE / HEXANE / HEPTANE / PENTANE / PENTADECANE / N-BUTANE / N-OCTANE / UNDECANE / Glycine receptor alpha 1 / Glycine receptor beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsZhu, H. / Gouaux, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100400 United States
CitationJournal: Nature / Year: 2021
Title: Architecture and assembly mechanism of native glycine receptors.
Authors: Hongtao Zhu / Eric Gouaux /
Abstract: Glycine receptors (GlyRs) are pentameric, 'Cys-loop' receptors that form chloride-permeable channels and mediate fast inhibitory signalling throughout the central nervous system. In the spinal cord ...Glycine receptors (GlyRs) are pentameric, 'Cys-loop' receptors that form chloride-permeable channels and mediate fast inhibitory signalling throughout the central nervous system. In the spinal cord and brainstem, GlyRs regulate locomotion and cause movement disorders when mutated. However, the stoichiometry of native GlyRs and the mechanism by which they are assembled remain unclear, despite extensive investigation. Here we report cryo-electron microscopy structures of native GlyRs from pig spinal cord and brainstem, revealing structural insights into heteromeric receptors and their predominant subunit stoichiometry of 4α:1β. Within the heteromeric pentamer, the β(+)-α(-) interface adopts a structure that is distinct from the α(+)-α(-) and α(+)-β(-) interfaces. Furthermore, the β-subunit contains a unique phenylalanine residue that resides within the pore and disrupts the canonical picrotoxin site. These results explain why inclusion of the β-subunit breaks receptor symmetry and alters ion channel pharmacology. We also find incomplete receptor complexes and, by elucidating their structures, reveal the architectures of partially assembled α-trimers and α-tetramers.
History
DepositionApr 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 1, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
J: 3D1 Fab Light Chain
G: 3D1 Fab Heavy Chain
K: 3D1 Fab Light Chain
F: 3D1 Fab Heavy Chain
M: 3D1 Fab Light Chain
L: 3D1 Fab Heavy Chain
I: 3D1 Fab Light Chain
H: 3D1 Fab Heavy Chain
D: Glycine receptor alpha 1
A: Glycine receptor alpha 1
B: Glycine receptor alpha 1
C: Glycine receptor alpha 1
E: Glycine receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,51766
Polymers361,13813
Non-polymers8,37953
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 DABCE

#3: Protein
Glycine receptor alpha 1


Mass: 51507.523 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RQB7
#4: Protein Glycine receptor beta


Mass: 56200.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6KBX4

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Antibody , 2 types, 8 molecules JKMIGFLH

#1: Antibody
3D1 Fab Light Chain


Mass: 11743.124 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Rattus norvegicus (Norway rat)
#2: Antibody
3D1 Fab Heavy Chain


Mass: 12983.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Rattus norvegicus (Norway rat)

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Sugars , 4 types, 5 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 11 types, 48 molecules

#9: Chemical
ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C7H16
#10: Chemical ChemComp-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H20
#11: Chemical
ChemComp-LNK / PENTANE


Mass: 72.149 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C5H12
#12: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32
#13: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#14: Chemical
ChemComp-NBU / N-BUTANE


Mass: 58.122 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10
#15: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#16: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26
#17: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#18: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14
#19: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Native heteromeric glycine receptor bound with 3D1 fabCOMPLEX#1-#40MULTIPLE SOURCES
2Native heteromeric glycine receptorCOMPLEX#3-#41NATURAL
33D1 fabCOMPLEX#1-#21RECOMBINANT
Molecular weightValue: 0.5 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Sus scrofa (pig)9823
33Rattus norvegicus (Norway rat)10116
Source (recombinant)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 8
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 / Cs: 2.7 mm
Image recordingElectron dose: 28.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 527075 / Symmetry type: POINT

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