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Yorodumi- EMDB-29019: Alpha1/BetaB Heteromeric Glycine Receptor in 1 mM Glycine 20 uM I... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29019 | ||||||||||||
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Title | Alpha1/BetaB Heteromeric Glycine Receptor in 1 mM Glycine 20 uM Ivermectin State | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Glycine / Channel / Ivermectin / Pentameric / MEMBRANE PROTEIN | ||||||||||||
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 / protein localization / 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: 3.0 Å | ||||||||||||
Authors | Gibbs E / Chakrapani S | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Chem Biol / Year: 2024 Title: High-throughput reprogramming of an NRPS condensation domain. Authors: Ines B Folger / Natália F Frota / Angelos Pistofidis / David L Niquille / Douglas A Hansen / T Martin Schmeing / Donald Hilvert / Abstract: Engineered biosynthetic assembly lines could revolutionize the sustainable production of bioactive natural product analogs. Although yeast display is a proven, powerful tool for altering the ...Engineered biosynthetic assembly lines could revolutionize the sustainable production of bioactive natural product analogs. Although yeast display is a proven, powerful tool for altering the substrate specificity of gatekeeper adenylation domains in nonribosomal peptide synthetases (NRPSs), comparable strategies for other components of these megaenzymes have not been described. Here we report a high-throughput approach for engineering condensation (C) domains responsible for peptide elongation. We show that a 120-kDa NRPS module, displayed in functional form on yeast, can productively interact with an upstream module, provided in solution, to produce amide products tethered to the yeast surface. Using this system to screen a large C-domain library, we reprogrammed a surfactin synthetase module to accept a fatty acid donor, increasing catalytic efficiency for this noncanonical substrate >40-fold. Because C domains can function as selectivity filters in NRPSs, this methodology should facilitate the precision engineering of these molecular assembly lines. #2: 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_29019.map.gz | 51.5 MB | EMDB map data format | |
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Header (meta data) | emd-29019-v30.xml emd-29019.xml | 24.4 KB 24.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29019_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_29019.png | 84.4 KB | ||
Masks | emd_29019_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-29019.cif.gz | 7.2 KB | ||
Others | emd_29019_half_map_1.map.gz emd_29019_half_map_2.map.gz | 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29019 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29019 | HTTPS FTP |
-Validation report
Summary document | emd_29019_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_29019_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_29019_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_29019_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29019 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29019 | HTTPS FTP |
-Related structure data
Related structure data | 8fe1MC 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_29019.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: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29019_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29019_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29019_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 / 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 UniProtKB: Glycine receptor subunit alphaZ1 |
-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 UniProtKB: Glycine receptor beta subunit 2 |
-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: |
-Macromolecule #5: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)...
Macromolecule | Name: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H- ...Name: (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside type: ligand / ID: 5 / Number of copies: 5 / Formula: IVM |
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Molecular weight | Theoretical: 875.093 Da |
-Macromolecule #6: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 8 / Formula: PX4 |
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Molecular weight | Theoretical: 678.94 Da |
Chemical component information | ChemComp-PX4: |
-Macromolecule #7: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 7 / Number of copies: 28 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ChemComp-PLM: |
-Macromolecule #8: DECANE
Macromolecule | Name: DECANE / type: ligand / ID: 8 / Number of copies: 1 / Formula: D10 |
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Molecular weight | Theoretical: 142.282 Da |
Chemical component information | ChemComp-D10: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | .1 mg/mL | |||||||||||||||||||||
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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 | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||||||||
Details | Single Particles |
-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: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |