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Yorodumi- EMDB-26141: Alpha1/BetaB Heteromeric Glycine Receptor in Glycine-Bound State -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26141 | |||||||||
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Title | Alpha1/BetaB Heteromeric Glycine Receptor in Glycine-Bound State | |||||||||
Map data | ||||||||||
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 / regulation of neuron differentiation / glycine binding / chloride channel complex / ligand-gated monoatomic ion channel activity ...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 / regulation of neuron differentiation / glycine binding / chloride channel complex / ligand-gated monoatomic ion channel activity / neuropeptide signaling pathway / response to amino acid / monoatomic ion transport / chloride transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / central nervous system development / cellular response to amino acid stimulus / protein localization / transmembrane signaling receptor activity / perikaryon / postsynaptic membrane / neuron projection / dendrite / synapse / zinc ion binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Danio rerio (zebrafish) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Gibbs E / Chakrapani S / Kumar A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Conformational transitions and allosteric modulation in a heteromeric glycine receptor Authors: Gibbs E / Klemm E / Seiferth D / Kumar A / Ilca SL / Biggin PC / Chakrapani S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26141.map.gz | 52.2 MB | EMDB map data format | |
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Header (meta data) | emd-26141-v30.xml emd-26141.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26141_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_26141.png | 80.6 KB | ||
Masks | emd_26141_msk_1.map | 103 MB | Mask map | |
Others | emd_26141_half_map_1.map.gz emd_26141_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26141 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26141 | HTTPS FTP |
-Related structure data
Related structure data | 7tviMC 7tu9C 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_26141.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26141_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26141_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26141_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor
Entire | Name: Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor |
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Components |
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-Supramolecule #1: Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor
Supramolecule | Name: Zebrafish Alpha1 BetaB Heteromeric Glycine Receptor / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: Glycine receptor subunit alphaZ1
Macromolecule | Name: Glycine receptor subunit alphaZ1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Molecular weight | Theoretical: 52.537598 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
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 #2: Glycine receptor beta subunit 2
Macromolecule | Name: Glycine receptor beta subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Molecular weight | Theoretical: 65.820281 KDa |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Sequence | String: MKALKVIFML LIICLWMEGG FTKEKSAKKW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGS WSHPQFEKEN LYFQGEKSAK KGKKKGKQVY CPSQLSSEDL ARVPANSTSN ILNKLLITYD PRIRPNFKGI P VEDRVNIF ...String: MKALKVIFML LIICLWMEGG FTKEKSAKKW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGSW SHPQFEKGGG SGGGSGGGS WSHPQFEKEN LYFQGEKSAK KGKKKGKQVY CPSQLSSEDL ARVPANSTSN ILNKLLITYD PRIRPNFKGI P VEDRVNIF INSFGSIQET TMDYRVNIFL RQRWNDPRLR LPQDFKSDSL TVDPKMFKCL WKPDLFFANE KSANFHDVTQ EN ILLFIFR NGDVLISMRL SVTLSCPLDL TLFPMDTQRC KMQLESFGYT TDDLQFMWQS GDPVQMDEIA LPQFDIKQED IEY GNCTKY YAGTGYYTCV EVIFTLRRQV GFYMMGVYAP TLLIVVLSWL SFWINPDASA ARVPLGILSV LSLSSECTSL ASEL PKVSY VKAIDIWLIA CLLFGFASLV EYAVVQVMLN SPKLLEAERA KIATKEKAEG KTPAKNTING MGSTPIHVST LQVTE TRCK KVCTSKSDLR TNDFSIVGSL PRDFELSNFD CYGKPIEVGS AFSKSQAKNN KKPPPPKPVI PSAAKRIDLY ARALFP FSF LFFNVIYWSV YLENLYFQGT ETSQVAPA |
-Macromolecule #3: GLYCINE
Macromolecule | Name: GLYCINE / type: ligand / ID: 3 / Number of copies: 5 / Formula: GLY |
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Molecular weight | Theoretical: 75.067 Da |
Chemical component information | ChemComp-GLY: |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | Single Particle |
-Electron microscopy #1
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm |
Microscopy ID | 1 |
Image recording | Image recording ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #1~
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm |
Microscopy ID | 1 |
Image recording | Image recording ID: 2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |