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Yorodumi- EMDB-11657: CryoEM structure of a human gamma-aminobutyric acid receptor, the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11657 | |||||||||||||||||||||
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Title | CryoEM structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3 homopentamer, in complex with histamine and megabody Mb25 in lipid nanodisc | |||||||||||||||||||||
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Function / homology | Function and homology information cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / Signaling by ERBB4 / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane ...cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / Signaling by ERBB4 / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / neurotransmitter receptor activity / roof of mouth development / chloride channel complex / transmembrane transporter complex / chloride transmembrane transport / cytoplasmic vesicle membrane / neuron projection / synapse / signal transduction / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.7 Å | |||||||||||||||||||||
Authors | Nakane T / Kotecha A / Sente A / Yamashita K / McMullan G / Masiulis S / Brown PMGE / Grigoras IT / Malinauskaite L / Malinauskas T ...Nakane T / Kotecha A / Sente A / Yamashita K / McMullan G / Masiulis S / Brown PMGE / Grigoras IT / Malinauskaite L / Malinauskas T / Miehling J / Yu L / Karia D / Pechnikova EV / de Jong E / Keizer J / Bischoff M / McCormack J / Tiemeijer P / Hardwick SW / Chirgadze DY / Murshudov G / Aricescu AR / Scheres SHW | |||||||||||||||||||||
Funding support | United Kingdom, 6 items
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Citation | Journal: Nature / Year: 2020 Title: Single-particle cryo-EM at atomic resolution. Authors: Takanori Nakane / Abhay Kotecha / Andrija Sente / Greg McMullan / Simonas Masiulis / Patricia M G E Brown / Ioana T Grigoras / Lina Malinauskaite / Tomas Malinauskas / Jonas Miehling / ...Authors: Takanori Nakane / Abhay Kotecha / Andrija Sente / Greg McMullan / Simonas Masiulis / Patricia M G E Brown / Ioana T Grigoras / Lina Malinauskaite / Tomas Malinauskas / Jonas Miehling / Tomasz Uchański / Lingbo Yu / Dimple Karia / Evgeniya V Pechnikova / Erwin de Jong / Jeroen Keizer / Maarten Bischoff / Jamie McCormack / Peter Tiemeijer / Steven W Hardwick / Dimitri Y Chirgadze / Garib Murshudov / A Radu Aricescu / Sjors H W Scheres / Abstract: The three-dimensional positions of atoms in protein molecules define their structure and their roles in biological processes. The more precisely atomic coordinates are determined, the more chemical ...The three-dimensional positions of atoms in protein molecules define their structure and their roles in biological processes. The more precisely atomic coordinates are determined, the more chemical information can be derived and the more mechanistic insights into protein function may be inferred. Electron cryo-microscopy (cryo-EM) single-particle analysis has yielded protein structures with increasing levels of detail in recent years. However, it has proved difficult to obtain cryo-EM reconstructions with sufficient resolution to visualize individual atoms in proteins. Here we use a new electron source, energy filter and camera to obtain a 1.7 Å resolution cryo-EM reconstruction for a human membrane protein, the β3 GABA receptor homopentamer. Such maps allow a detailed understanding of small-molecule coordination, visualization of solvent molecules and alternative conformations for multiple amino acids, and unambiguous building of ordered acidic side chains and glycans. Applied to mouse apoferritin, our strategy led to a 1.22 Å resolution reconstruction that offers a genuine atomic-resolution view of a protein molecule using single-particle cryo-EM. Moreover, the scattering potential from many hydrogen atoms can be visualized in difference maps, allowing a direct analysis of hydrogen-bonding networks. Our technological advances, combined with further approaches to accelerate data acquisition and improve sample quality, provide a route towards routine application of cryo-EM in high-throughput screening of small molecule modulators and structure-based drug discovery. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11657.map.gz | 167.2 MB | EMDB map data format | |
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Header (meta data) | emd-11657-v30.xml emd-11657.xml | 25 KB 25 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11657_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_11657.png | 71.8 KB | ||
Masks | emd_11657_msk_1.map | 178 MB | Mask map | |
Others | emd_11657_half_map_1.map.gz emd_11657_half_map_2.map.gz | 140.7 MB 140.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11657 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11657 | HTTPS FTP |
-Validation report
Summary document | emd_11657_validation.pdf.gz | 352.2 KB | Display | EMDB validaton report |
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Full document | emd_11657_full_validation.pdf.gz | 351.4 KB | Display | |
Data in XML | emd_11657_validation.xml.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11657 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11657 | HTTPS FTP |
-Related structure data
Related structure data | 7a5vMC 7a4mC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10500 (Title: High resolution structure of GABAAR beta3 homopentamer Data size: 13.0 TB Data #1: CFEG, Falcon4, with 5 eV filter [micrographs - multiframe] Data #2: CFEG, Falcon4, with 5 eV filter, without objective aperture [micrographs - multiframe] Data #3: XFEG, Falcon3, without filter [micrographs - multiframe] Data #4: XFEG, Falcon4, with filter but retracted slit [micrographs - multiframe] Data #5: XFEG, Falcon4, with 3 eV filter [micrographs - multiframe] Data #6: XFEG, Falcon4, with 5 eV filter [micrographs - multiframe] Data #7: XFEG, Falcon4, with 3 eV filter [micrographs - multiframe] Data #8: XFEG, K3, without filter [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11657.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8117 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11657_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11657_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11657_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human GABA(A)R-beta3 homopentamer in complex with Megabody-25 in ...
+Supramolecule #1: Human GABA(A)R-beta3 homopentamer in complex with Megabody-25 in ...
+Supramolecule #2: Human GABA(A)R-beta3 homopentamer
+Supramolecule #3: Megabody-25
+Macromolecule #1: Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyri...
+Macromolecule #2: Megabody Mb25
+Macromolecule #5: HEXADECANE
+Macromolecule #6: DECANE
+Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #8: N-OCTANE
+Macromolecule #9: HISTAMINE
+Macromolecule #10: CHLORIDE ION
+Macromolecule #11: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 287 K / Instrument: LEICA PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 40.0 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: 1.1 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7a5v: |