+Open data
-Basic information
Entry | Database: PDB / ID: 8jmt | |||||||||
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Title | Structure of the adhesion GPCR ADGRL3 in the apo state | |||||||||
Components | Adhesion G protein-coupled receptor L3,Soluble cytochrome b562 | |||||||||
Keywords | MEMBRANE PROTEIN / ADGRL3 / Apo form | |||||||||
Function / homology | Function and homology information G protein-coupled receptor activity / electron transport chain / carbohydrate binding / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / iron ion binding / heme binding / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Tao, Y. / Guo, Q. / He, B. / Zhong, Y. | |||||||||
Funding support | China, 1items
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Citation | Journal: Nat Chem Biol / Year: 2024 Title: A method for structure determination of GPCRs in various states. Authors: Qiong Guo / Binbin He / Yixuan Zhong / Haizhan Jiao / Yinhang Ren / Qinggong Wang / Qiangqiang Ge / Yongxiang Gao / Xiangyu Liu / Yang Du / Hongli Hu / Yuyong Tao / Abstract: G-protein-coupled receptors (GPCRs) are a class of integral membrane proteins that detect environmental cues and trigger cellular responses. Deciphering the functional states of GPCRs induced by ...G-protein-coupled receptors (GPCRs) are a class of integral membrane proteins that detect environmental cues and trigger cellular responses. Deciphering the functional states of GPCRs induced by various ligands has been one of the primary goals in the field. Here we developed an effective universal method for GPCR cryo-electron microscopy structure determination without the need to prepare GPCR-signaling protein complexes. Using this method, we successfully solved the structures of the β-adrenergic receptor (βAR) bound to antagonistic and agonistic ligands and the adhesion GPCR ADGRL3 in the apo state. For βAR, an intermediate state stabilized by the partial agonist was captured. For ADGRL3, the structure revealed that inactive ADGRL3 adopts a compact fold and that large unusual conformational changes on both the extracellular and intracellular sides are required for activation of adhesion GPCRs. We anticipate that this method will open a new avenue for understanding GPCR structure‒function relationships and drug development. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jmt.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jmt.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 8jmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jmt_validation.pdf.gz | 980.7 KB | Display | wwPDB validaton report |
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Full document | 8jmt_full_validation.pdf.gz | 983 KB | Display | |
Data in XML | 8jmt_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 8jmt_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/8jmt ftp://data.pdbj.org/pub/pdb/validation_reports/jm/8jmt | HTTPS FTP |
-Related structure data
Related structure data | 36426MC 8j7eC 8jj8C 8jjlC 8jjoC 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: 85439.922 Da / Num. of mol.: 1 / Mutation: T364A/M566W/H654I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: ADGRL3, cybC / Production host: Homo sapiens (human) / References: UniProt: E7ES20, UniProt: P0ABE7 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ADGRL3-mBRIL complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 706010 / Symmetry type: POINT | ||||||||||||||||||||||||
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