1YUK

The crystal structure of the PSI/Hybrid domain/ I-EGF1 segment from the human integrin beta2 at 1.8 resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin {beta}2 Subunit at 1.8-A Resolution

Shi, M.Sundramurthy, K.Liu, B.Tan, S.M.Law, S.K.Lescar, J.

(2005) J.Biol.Chem. 280: 30586-30593

  • DOI: 10.1074/jbc.M502525200
  • Also Cited By: 5E6V

  • PubMed Abstract: 
  • Integrins are modular (alphabeta) heterodimeric proteins that mediate cell adhesion and convey signals across the plasma membrane. Interdomain motions play a key role in signal transduction by propagating structural changes through the molecule, thus ...

    Integrins are modular (alphabeta) heterodimeric proteins that mediate cell adhesion and convey signals across the plasma membrane. Interdomain motions play a key role in signal transduction by propagating structural changes through the molecule, thus controlling the activation state and adhesive properties of the integrin. We expressed a soluble fragment of the human integrin beta2 subunit comprising the plexin-semaphorin-integrin domain (PSI)/hybrid domain/I-EGF1 fragment and present its crystal structure at 1.8-A resolution. The structure reveals an elongated molecule with a rigid architecture stabilized by nine disulfide bridges. The PSI domain is located centrally and participates in the formation of extended interfaces with the hybrid domain and I-EGF1 domains, respectively. The hybrid domain/PSI interface involves the burial of an Arg residue, and contacts between PSI and I-EGF1 are mainly mediated by well conserved Arg and Trp residues. Conservation of key interacting residues across the various integrin beta subunits sequences suggests that our structure represents a good model for the entire integrin family. Superposition with the integrin beta3 receptor in its bent conformation suggests that an articulation point is present at the linkage between its I-EGF1 and I-EGF2 modules and underlines the importance of this region for the control of integrin-mediated cell adhesion.


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-2 A chain
A
103Homo sapiensMutation(s): 0 
Gene Names: ITGB2 (CD18, MFI7)
Find proteins for P05107 (Homo sapiens)
Go to Gene View: ITGB2
Go to UniProtKB:  P05107
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-2 B chain
B
120Homo sapiensMutation(s): 0 
Gene Names: ITGB2 (CD18, MFI7)
Find proteins for P05107 (Homo sapiens)
Go to Gene View: ITGB2
Go to UniProtKB:  P05107
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
A, B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.600α = 90.00
b = 31.818β = 91.20
c = 74.950γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance