5E6W

Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 2P28 - determined by Shi, M., Foo, S.Y., Tan, S.M., Mitchell, E.P., Law, S.K.A., Lescar, J.  

Literature

Leukocyte integrin alpha L beta 2 headpiece structures: The alpha I domain, the pocket for the internal ligand, and concerted movements of its loops.

Sen, M.Springer, T.A.

(2016) Proc.Natl.Acad.Sci.USA 113: 2940-2945

  • DOI: 10.1073/pnas.1601379113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • High-resolution crystal structures of the headpiece of lymphocyte function-associated antigen-1 (integrin αLβ2) reveal how the αI domain interacts with its platform formed by the α-subunit β-propeller and β-subunit βI domains. The αLβ2 structures com ...

    High-resolution crystal structures of the headpiece of lymphocyte function-associated antigen-1 (integrin αLβ2) reveal how the αI domain interacts with its platform formed by the α-subunit β-propeller and β-subunit βI domains. The αLβ2 structures compared with αXβ2 structures show that the αI domain, tethered through its N-linker and a disulfide to a stable β-ribbon pillar near the center of the platform, can undergo remarkable pivoting and tilting motions that appear buffered by N-glycan decorations that differ between αL and αX subunits. Rerefined β2 integrin structures reveal details including pyroglutamic acid at the β2 N terminus and bending within the EGF1 domain. Allostery is relayed to the αI domain by an internal ligand that binds to a pocket at the interface between the β-propeller and βI domains. Marked differences between the αL and αX subunit β-propeller domains concentrate near the binding pocket and αI domain interfaces. Remarkably, movement in allostery in the βI domain of specificity determining loop 1 (SDL1) causes concerted movement of SDL2 and thereby tightens the binding pocket for the internal ligand.


    Related Citations: 
    • A structural hypothesis for the transition between bent and extended conformations of the leukocyte beta2 integrins.
      Shi, M.,Foo, S.Y.,Tan, S.M.,Mitchell, E.P.,Law, S.K.,Lescar, J.
      (2007) J. Biol. Chem. 282: 30198


    Organizational Affiliation

    Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA 02115; Department of Biology and Biochemistry, University of Houston, Houston, TX 77204.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-2
A
317Homo 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
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.227 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 52.260α = 90.00
b = 52.260β = 90.00
c = 423.924γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesNCI CA031798

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references
  • Version 1.2: 2016-05-11
    Type: Database references
  • Version 1.3: 2017-03-15
    Type: Database references, Experimental preparation, Other
  • Version 1.4: 2017-09-27
    Type: Author supporting evidence