5E6V

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

Summary for 5E6V

• Entry DOI: 10.2210/pdb5e6v/pdb
• Descriptor: Integrin beta-2, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: lymphocyte function-associated antigen-1, lfa-1, cell adhesion
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 25968.20

Authors

Sen, M.,Springer, T.A. (deposition date: 2015-10-10, release date: 2016-03-02, Last modification date: 2024-11-06)

Primary citation

Sen, M.,Springer, T.A.
Leukocyte integrin alpha L beta 2 headpiece structures: The alpha I domain, the pocket for the internal ligand, and concerted movements of its loops.
Proc.Natl.Acad.Sci.USA, 113:2940-2945, 2016

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 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.

PubMed: 26936951
DOI: 10.1073/pnas.1601379113

Experimental method

X-RAY DIFFRACTION (1.8 Å)