+Open data
-Basic information
Entry | Database: PDB / ID: 8ikj | ||||||
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Title | Cryo-EM structure of the inactive CD97 | ||||||
Components | Adhesion G protein-coupled receptor E5,Soluble cytochrome b562,Adhesion G protein-coupled receptor E5 subunit beta | ||||||
Keywords | MEMBRANE PROTEIN / adhension GPCR / CD97 / inactive | ||||||
Function / homology | Function and homology information Class B/2 (Secretin family receptors) / secretory granule membrane / G protein-coupled receptor activity / electron transport chain / adenylate cyclase-activating G protein-coupled receptor signaling pathway / transmembrane signaling receptor activity / cell-cell signaling / periplasmic space / electron transfer activity / cell surface receptor signaling pathway ...Class B/2 (Secretin family receptors) / secretory granule membrane / G protein-coupled receptor activity / electron transport chain / adenylate cyclase-activating G protein-coupled receptor signaling pathway / transmembrane signaling receptor activity / cell-cell signaling / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / cell adhesion / inflammatory response / iron ion binding / immune response / G protein-coupled receptor signaling pathway / focal adhesion / calcium ion binding / heme binding / Neutrophil degranulation / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Mao, C. / Zhao, R. / Dong, Y. / Gao, M. / Chen, L. / Zhang, C. / Xiao, P. / Guo, J. / Qin, J. / Shen, D. ...Mao, C. / Zhao, R. / Dong, Y. / Gao, M. / Chen, L. / Zhang, C. / Xiao, P. / Guo, J. / Qin, J. / Shen, D. / Ji, S. / Zang, S. / Zhang, H. / Wang, W. / Shen, Q. / Sun, P. / Zhang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Mol Cell / Year: 2024 Title: Conformational transitions and activation of the adhesion receptor CD97. Authors: Chunyou Mao / Ru-Jia Zhao / Ying-Jun Dong / Mingxin Gao / Li-Nan Chen / Chao Zhang / Peng Xiao / Jia Guo / Jiao Qin / Dan-Dan Shen / Su-Yu Ji / Shao-Kun Zang / Huibing Zhang / Wei-Wei Wang / ...Authors: Chunyou Mao / Ru-Jia Zhao / Ying-Jun Dong / Mingxin Gao / Li-Nan Chen / Chao Zhang / Peng Xiao / Jia Guo / Jiao Qin / Dan-Dan Shen / Su-Yu Ji / Shao-Kun Zang / Huibing Zhang / Wei-Wei Wang / Qingya Shen / Jin-Peng Sun / Yan Zhang / Abstract: Adhesion G protein-coupled receptors (aGPCRs) are evolutionarily ancient receptors involved in a variety of physiological and pathophysiological processes. Modulators of aGPCR, particularly ...Adhesion G protein-coupled receptors (aGPCRs) are evolutionarily ancient receptors involved in a variety of physiological and pathophysiological processes. Modulators of aGPCR, particularly antagonists, hold therapeutic promise for diseases like cancer and immune and neurological disorders. Hindered by the inactive state structural information, our understanding of antagonist development and aGPCR activation faces challenges. Here, we report the cryo-electron microscopy structures of human CD97, a prototypical aGPCR that plays crucial roles in immune system, in its inactive apo and G13-bound fully active states. Compared with other family GPCRs, CD97 adopts a compact inactive conformation with a constrained ligand pocket. Activation induces significant conformational changes for both extracellular and intracellular sides, creating larger cavities for Stachel sequence binding and G13 engagement. Integrated with functional and metadynamics analyses, our study provides significant mechanistic insights into the activation and signaling of aGPCRs, paving the way for future drug discovery efforts. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ikj.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ikj.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ikj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ikj_validation.pdf.gz | 768.3 KB | Display | wwPDB validaton report |
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Full document | 8ikj_full_validation.pdf.gz | 770.8 KB | Display | |
Data in XML | 8ikj_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 8ikj_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/8ikj ftp://data.pdbj.org/pub/pdb/validation_reports/ik/8ikj | HTTPS FTP |
-Related structure data
Related structure data | 35514MC 8iklC 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: 72551.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli) Gene: ADGRE5, CD97, cybC / Production host: Fusarium sinicum (fungus) / References: UniProt: P48960, UniProt: P0ABE7 | ||
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#2: Sugar | 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
Component | Name: Adhesion G protein-coupled receptor E5 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Fusarium sinicum (fungus) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 540042 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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