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Yorodumi- EMDB-26316: A novel compound mimics the structural and functional effects of ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26316 | |||||||||
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Title | A novel compound mimics the structural and functional effects of the full agonist glycine on glycine channels-open state | |||||||||
Map data | LocScale sharpened map | |||||||||
Sample |
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Function / homology | Function and homology information Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / synaptic transmission, glycinergic / cellular response to ethanol / cellular response to zinc ion / neurotransmitter receptor activity / regulation of neuron differentiation / glycine binding / chloride channel complex ...Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated ion channel activity / extracellularly glycine-gated chloride channel activity / synaptic transmission, glycinergic / cellular response to ethanol / cellular response to zinc ion / neurotransmitter receptor activity / regulation of neuron differentiation / glycine binding / chloride channel complex / ligand-gated monoatomic ion channel activity / transmembrane transporter complex / neuropeptide signaling pathway / response to amino acid / monoatomic ion transport / chloride transmembrane transport / central nervous system development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cellular response to amino acid stimulus / transmembrane signaling receptor activity / postsynaptic membrane / perikaryon / neuron projection / synapse / dendrite / zinc ion binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Danio rerio (zebrafish) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Zhu H / Gouaux E | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: A novel compound mimics the structural and functional effects of the full agonist glycine on glycine channels-open state Authors: Zhu H / Gouaux E | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26316.map.gz | 117.2 MB | EMDB map data format | |
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Header (meta data) | emd-26316-v30.xml emd-26316.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | emd_26316.png | 104.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26316 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26316 | HTTPS FTP |
-Validation report
Summary document | emd_26316_validation.pdf.gz | 336 KB | Display | EMDB validaton report |
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Full document | emd_26316_full_validation.pdf.gz | 335.6 KB | Display | |
Data in XML | emd_26316_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_26316_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26316 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26316 | HTTPS FTP |
-Related structure data
Related structure data | 7u2nMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26316.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | LocScale sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.831 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Pentameric glycine receptor bound with aminomethanesulfonic acid
Entire | Name: Pentameric glycine receptor bound with aminomethanesulfonic acid |
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Components |
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-Supramolecule #1: Pentameric glycine receptor bound with aminomethanesulfonic acid
Supramolecule | Name: Pentameric glycine receptor bound with aminomethanesulfonic acid type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Molecular weight | Theoretical: 250 kDa/nm |
-Macromolecule #1: Glycine receptor subunit alphaZ1
Macromolecule | Name: Glycine receptor subunit alphaZ1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Molecular weight | Theoretical: 52.537598 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MFALGIYLWE TIVFFSLAAS QQAAARKAAS PMPPSEFLDK LMGKVSGYDA RIRPNFKGPP VNVTCNIFIN SFGSIAETTM DYRVNIFLR QQWNDPRLAY SEYPDDSLDL DPSMLDSIWK PDLFFANEKG ANFHEVTTDN KLLRISKNGN VLYSIRITLV L ACPMDLKN ...String: MFALGIYLWE TIVFFSLAAS QQAAARKAAS PMPPSEFLDK LMGKVSGYDA RIRPNFKGPP VNVTCNIFIN SFGSIAETTM DYRVNIFLR QQWNDPRLAY SEYPDDSLDL DPSMLDSIWK PDLFFANEKG ANFHEVTTDN KLLRISKNGN VLYSIRITLV L ACPMDLKN FPMDVQTCIM QLESFGYTMN DLIFEWDEKG AVQVADGLTL PQFILKEEKD LRYCTKHYNT GKFTCIEARF HL ERQMGYY LIQMYIPSLL IVILSWVSFW INMDAAPARV GLGITTVLTM TTQSSGSRAS LPKVSYVKAI DIWMAVCLLF VFS ALLEYA AVNFIARQHK ELLRFQRRRR HLKEDEAGDG RFSFAAYGMG PACLQAKDGM AIKGNNNNAP TSTNPPEKTV EEMR KLFIS RAKRIDTVSR VAFPLVFLIF NIFYWITYKI IRSEDIHKQL VPRGSHHHHH HHH |
-Macromolecule #3: aminomethanesulfonic acid
Macromolecule | Name: aminomethanesulfonic acid / type: ligand / ID: 3 / Number of copies: 5 / Formula: L2L |
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Molecular weight | Theoretical: 111.12 Da |
Chemical component information | ChemComp-L2L: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.04 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 200.0 nm |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 34.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 22.0 µm / Nominal defocus min: 12.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207486 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |