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Yorodumi- PDB-7ul3: CryoEM Structure of Inactive H2R Bound to Famotidine, Nb6M, and NabFab -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ul3 | ||||||
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Title | CryoEM Structure of Inactive H2R Bound to Famotidine, Nb6M, and NabFab | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Antagonist / Complex | ||||||
Function / homology | Function and homology information gastric acid secretion / Histamine receptors / histamine receptor activity / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / positive regulation of vasoconstriction / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G alpha (s) signalling events / chemical synaptic transmission / immune response ...gastric acid secretion / Histamine receptors / histamine receptor activity / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / positive regulation of vasoconstriction / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G alpha (s) signalling events / chemical synaptic transmission / immune response / synapse / dendrite / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Robertson, M.J. / Skiniotis, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Structure determination of inactive-state GPCRs with a universal nanobody. Authors: Michael J Robertson / Makaía M Papasergi-Scott / Feng He / Alpay B Seven / Justin G Meyerowitz / Ouliana Panova / Maria Claudia Peroto / Tao Che / Georgios Skiniotis / Abstract: Cryogenic electron microscopy (cryo-EM) has widened the field of structure-based drug discovery by allowing for routine determination of membrane protein structures previously intractable. Despite ...Cryogenic electron microscopy (cryo-EM) has widened the field of structure-based drug discovery by allowing for routine determination of membrane protein structures previously intractable. Despite representing one of the largest classes of therapeutic targets, most inactive-state G protein-coupled receptors (GPCRs) have remained inaccessible for cryo-EM because their small size and membrane-embedded nature impedes projection alignment for high-resolution map reconstructions. Here we demonstrate that the same single-chain camelid antibody (nanobody) recognizing a grafted intracellular loop can be used to obtain cryo-EM structures of inactive-state GPCRs at resolutions comparable or better than those obtained by X-ray crystallography. Using this approach, we obtained structures of neurotensin 1 receptor bound to antagonist SR48692, μ-opioid receptor bound to alvimopan, apo somatostatin receptor 2 and histamine receptor 2 bound to famotidine. We expect this rapid, straightforward approach to facilitate the broad exploration of GPCR inactive states without the need for extensive engineering and crystallization. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ul3.cif.gz | 140.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ul3.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ul3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ul3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7ul3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7ul3_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 7ul3_validation.cif.gz | 49.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/7ul3 ftp://data.pdbj.org/pub/pdb/validation_reports/ul/7ul3 | HTTPS FTP |
-Related structure data
Related structure data | 26590MC 7ul2C 7ul4C 7ul5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 44770.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HRH2, OPRK1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25021, UniProt: A0A8B8VNB6 |
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#2: Antibody | Mass: 14418.919 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
#3: Antibody | Mass: 25684.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
#4: Antibody | Mass: 23258.783 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
#5: Chemical | ChemComp-FO9 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 58.58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 365068 / Symmetry type: POINT |