3BN3

crystal structure of ICAM-5 in complex with aL I domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An unusual allosteric mobility of the C-terminal helix of a high-affinity alpha L integrin I domain variant bound to ICAM-5

Zhang, H.Casasnovas, J.M.Jin, M.Liu, J.H.Gahmberg, C.G.Springer, T.A.Wang, J.-h.

(2008) Mol.Cell 31: 432-437

  • DOI: 10.1016/j.molcel.2008.06.022

  • PubMed Abstract: 
  • Integrins are cell surface receptors that transduce signals bidirectionally across the plasma membrane. The key event of integrin signaling is the allosteric regulation between its ligand-binding site and the C-terminal helix (alpha7) of integrin's i ...

    Integrins are cell surface receptors that transduce signals bidirectionally across the plasma membrane. The key event of integrin signaling is the allosteric regulation between its ligand-binding site and the C-terminal helix (alpha7) of integrin's inserted (I) domain. A significant axial movement of the alpha7 helix is associated with the open, active conformation of integrins. We describe the crystal structure of an engineered high-affinity I domain from the integrin alpha(L)beta(2) (LFA-1) alpha subunit in complex with the N-terminal two domains of ICAM-5, an adhesion molecule expressed in telencephalic neurons. The finding that the alpha7 helix swings out and inserts into a neighboring I domain in an upside-down orientation in the crystals implies an intrinsically unusual mobility of this helix. This remarkable feature allows the alpha7 helix to trigger integrin's large-scale conformational changes with little energy penalty. It serves as a mechanistic example of how a weakly bound adhesion molecule works in signaling.


    Organizational Affiliation

    Department of Medical Oncology and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-L
A
180Homo sapiensMutation(s): 2 
Gene Names: ITGAL (CD11A)
Find proteins for P20701 (Homo sapiens)
Go to Gene View: ITGAL
Go to UniProtKB:  P20701
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Intercellular adhesion molecule 5
B
196Homo sapiensMutation(s): 0 
Gene Names: ICAM5 (TLCN, TLN)
Find proteins for Q9UMF0 (Homo sapiens)
Go to Gene View: ICAM5
Go to UniProtKB:  Q9UMF0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.793α = 90.00
b = 71.507β = 90.00
c = 143.871γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance