8ZJF | pdb_00008zjf

Cryo-EM structure of human integrin alpha-E beta-7


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZJF

This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structure of I domain-containing integrin alpha E beta 7.

Akasaka, H.Sato, D.Shihoya, W.Nureki, O.Kise, Y.

(2024) Biochem Biophys Res Commun 721: 150121-150121

  • DOI: https://doi.org/10.1016/j.bbrc.2024.150121
  • Primary Citation Related Structures: 
    8ZJF

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 223.18 kDa 
  • Atom Count: 10,917 
  • Modeled Residue Count: 1,419 
  • Deposited Residue Count: 2,024 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin beta-7A [auth B]826Homo sapiensMutation(s): 0 
Gene Names: ITGB7
UniProt & NIH Common Fund Data Resources
Find proteins for P26010 (Homo sapiens)
Explore P26010 
Go to UniProtKB:  P26010
PHAROS:  P26010
GTEx:  ENSG00000139626 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26010
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin alpha-EB [auth A]1,198Homo sapiensMutation(s): 0 
Gene Names: ITGAE
UniProt & NIH Common Fund Data Resources
Find proteins for P38570 (Homo sapiens)
Explore P38570 
Go to UniProtKB:  P38570
PHAROS:  P38570
GTEx:  ENSG00000083457 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38570
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P38570-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan22H02555

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-06-25
    Changes: Data collection