+Open data
-Basic information
Entry | Database: PDB / ID: 8zjf | ||||||
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Title | Cryo-EM structure of human integrin alpha-E beta-7 | ||||||
Components |
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Keywords | CELL ADHESION / Complex / Cryo-EM | ||||||
Function / homology | Function and homology information immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / T cell migration / leukocyte tethering or rolling / heterotypic cell-cell adhesion / integrin complex / cell adhesion mediated by integrin / leukocyte migration / receptor clustering ...immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / T cell migration / leukocyte tethering or rolling / heterotypic cell-cell adhesion / integrin complex / cell adhesion mediated by integrin / leukocyte migration / receptor clustering / Integrin cell surface interactions / cell adhesion molecule binding / substrate adhesion-dependent cell spreading / cell-matrix adhesion / integrin-mediated signaling pathway / cell-cell adhesion / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / virus receptor activity / receptor complex / cell adhesion / external side of plasma membrane / focal adhesion / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Akasaka, H. / Nureki, O. / Kise, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem Biophys Res Commun / Year: 2024 Title: Cryo-EM structure of I domain-containing integrin αEβ7. Authors: Hiroaki Akasaka / Dan Sato / Wataru Shihoya / Osamu Nureki / Yoshiaki Kise / Abstract: The integrin family is a transmembrane receptor that plays critical roles in the cell-cell and cell-extracellular matrix adhesion, signal transduction such as cell cycle regulation, organization of ...The integrin family is a transmembrane receptor that plays critical roles in the cell-cell and cell-extracellular matrix adhesion, signal transduction such as cell cycle regulation, organization of the intracellular cytoskeleton, and immune responses. Consequently, dysfunction of integrins is associated with a wide range of human diseases, including cancer and immune diseases, which makes integrins therapeutic targets for drug discovery. Here we report the cryo-EM structure of the human α-I domain-containing full-length integrin αEβ7, which is expressed in the leukocytes of the immune system and a drug target for inflammatory bowel disease (IBD). The structure reveals the half-bent conformation, an intermediate between the close and the open conformation, while the α-I domain responsible for the ligand binding covers the headpiece domain by a unique spatial arrangement. Our results provide the structural information for the drug design targeting IBD. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8zjf.cif.gz | 299.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zjf.ent.gz | 227.1 KB | Display | PDB format |
PDBx/mmJSON format | 8zjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zjf_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8zjf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8zjf_validation.xml.gz | 49.3 KB | Display | |
Data in CIF | 8zjf_validation.cif.gz | 74.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/8zjf ftp://data.pdbj.org/pub/pdb/validation_reports/zj/8zjf | HTTPS FTP |
-Related structure data
Related structure data | 60143MC 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: 90055.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB7 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P26010 | ||
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#2: Protein | Mass: 132436.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P38570 | ||
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Chemical | ChemComp-MG / | ||
#5: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Integrin alpha-E beta-7 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
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: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50.855 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 300397 / Symmetry type: POINT | ||||||||||||||||||||||||
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