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Yorodumi- EMDB-17793: Cryo-EM structure of cell-free synthesized human histamine H2 rec... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17793 | |||||||||||||||||||||
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Title | Cryo-EM structure of cell-free synthesized human histamine H2 receptor coupled to heterotrimeric Gs protein in lipid environment | |||||||||||||||||||||
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Sample |
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Keywords | GPCR / Cell-free / H2R / human histamine 2 receptor / active conformation / complex / detergent-free / lipid environment / MEMBRANE PROTEIN | |||||||||||||||||||||
Function / homology | Function and homology information gastric acid secretion / Histamine receptors / histamine receptor activity / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / PKA activation in glucagon signalling / hair follicle placode formation / intracellular transport / D1 dopamine receptor binding ...gastric acid secretion / Histamine receptors / histamine receptor activity / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / PKA activation in glucagon signalling / hair follicle placode formation / intracellular transport / D1 dopamine receptor binding / developmental growth / Hedgehog 'off' state / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of vasoconstriction / activation of adenylate cyclase activity / adenylate cyclase activator activity / trans-Golgi network membrane / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / bone development / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / platelet aggregation / Glucagon-type ligand receptors / cognition / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of GTPase activity / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / sensory perception of smell / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cold-induced thermogenesis / G alpha (i) signalling events / fibroblast proliferation / chemical synaptic transmission / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / immune response / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / dendrite / synapse / protein-containing complex binding / GTP binding / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||||||||
Authors | Schnelle K / Koeck Z / Persechino M / Umbach S / Schihada H / Januliene D / Parey K / Pockes S / Kolb P / Doetsch V ...Schnelle K / Koeck Z / Persechino M / Umbach S / Schihada H / Januliene D / Parey K / Pockes S / Kolb P / Doetsch V / Moeller A / Hilger D / Bernhard F | |||||||||||||||||||||
Funding support | Germany, 6 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Cryo-EM structure of cell-free synthesized human histamine 2 receptor/G complex in nanodisc environment. Authors: Zoe Köck / Kilian Schnelle / Margherita Persechino / Simon Umbach / Hannes Schihada / Dovile Januliene / Kristian Parey / Steffen Pockes / Peter Kolb / Volker Dötsch / Arne Möller / ...Authors: Zoe Köck / Kilian Schnelle / Margherita Persechino / Simon Umbach / Hannes Schihada / Dovile Januliene / Kristian Parey / Steffen Pockes / Peter Kolb / Volker Dötsch / Arne Möller / Daniel Hilger / Frank Bernhard / Abstract: Here we describe the cryo-electron microscopy structure of the human histamine 2 receptor (HR) in an active conformation with bound histamine and in complex with G heterotrimeric protein at an ...Here we describe the cryo-electron microscopy structure of the human histamine 2 receptor (HR) in an active conformation with bound histamine and in complex with G heterotrimeric protein at an overall resolution of 3.4 Å. The complex was generated by cotranslational insertion of the receptor into preformed nanodisc membranes using cell-free synthesis in E. coli lysates. Structural comparison with the inactive conformation of HR and the inactive and G-coupled active state of HR together with structure-guided functional experiments reveal molecular insights into the specificity of ligand binding and G protein coupling for this receptor family. We demonstrate lipid-modulated folding of cell-free synthesized HR, its agonist-dependent internalization and its interaction with endogenously synthesized HR and HR in HEK293 cells by applying a recently developed nanotransfer technique. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17793.map.gz | 84.6 MB | EMDB map data format | |
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Header (meta data) | emd-17793-v30.xml emd-17793.xml | 29.4 KB 29.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17793_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_17793.png | 140.1 KB | ||
Masks | emd_17793_msk_1.map | 91.1 MB | Mask map | |
Filedesc metadata | emd-17793.cif.gz | 7.6 KB | ||
Others | emd_17793_additional_1.map.gz emd_17793_additional_2.map.gz emd_17793_half_map_1.map.gz emd_17793_half_map_2.map.gz | 85.9 MB 45.1 MB 84.6 MB 84.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17793 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17793 | HTTPS FTP |
-Related structure data
Related structure data | 8pokMC 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_17793.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.924 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17793_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_17793_additional_1.map | ||||||||||||
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Density Histograms |
-Additional map: unsharpen map
File | emd_17793_additional_2.map | ||||||||||||
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Annotation | unsharpen map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17793_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17793_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : H2 receptor coupled to heterotrimeric Gs protein
+Supramolecule #1: H2 receptor coupled to heterotrimeric Gs protein
+Supramolecule #2: Histamine H2 receptor
+Supramolecule #3: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit...
+Supramolecule #4: Nanobody35
+Macromolecule #1: Histamine H2 receptor
+Macromolecule #2: Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit...
+Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #5: Nanobody35
+Macromolecule #6: HISTAMINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Specialist optics | Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV |
Sample stage | Cooling holder cryogen: NITROGEN |
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: 50.0 e/Å2 |