Electron tomography reveals diverse conformations of integrin αIIbβ3 in the active state

Iwasaki, Katsunori; Mitsuoka, Kaoru; Fujiyoshi, Yoshinori; Fujisawa, Yukio; Kikuchi, Masakazu; Sekiguchi, Kiyotoshi; Yamada, Takao

doi:10.1016/j.jsb.2005.03.005

Cited by 56 publications

(73 citation statements)

References 31 publications

(33 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Electron tomography of negatively stained, active, detergent-soluble α IIbβ3 purified on an RGD peptide affinity column reveals an extended conformation with >90% of particles showing an open headpiece structure that matches perfectly (60) the open, liganded α IIbβ3 headpiece crystal structure (36). In addition to structural investigations (33,34,36,43,60,61), integrin hybrid domain swing-out is supported by a range of other studies. Stabilizing the open headpiece by mutationally introducing an Nglycosylation site into the hybrid-β I domain interface increases ligand-binding affinity (62,63).…”

Section: Hybrid Domain Swing-out and Integrin Extensionsupporting

confidence: 56%

Structural Basis of Integrin Regulation and Signaling

Luo

Carman

Springer

2007

Annu. Rev. Immunol.

1,436

1,470

View full text Add to dashboard Cite

Integrins are cell adhesion molecules that mediate cell-cell, cell-extracellular matrix, and cellpathogen interactions. They play critical roles for the immune system in leukocyte trafficking and migration, immunological synapse formation, costimulation, and phagocytosis. Integrin adhesiveness can be dynamically regulated through a process termed inside-out signaling. In addition, ligand binding transduces signals from the extracellular domain to the cytoplasm in the classical outside-in direction. Recent structural, biochemical, and biophysical studies have greatly advanced our understanding of the mechanisms of integrin bidirectional signaling across the plasma membrane. Large-scale reorientations of the ectodomain of up to 200 Å couple to conformational change in ligand-binding sites and are linked to changes in α and β subunit transmembrane domain association. In this review, we focus on integrin structure as it relates to affinity modulation, ligand binding, outside-in signaling, and cell surface distribution dynamics.

show abstract

Section: Hybrid Domain Swing-out and Integrin Extensionsupporting

confidence: 56%

Structural Basis of Integrin Regulation and Signaling

Luo

Carman

Springer

2007

Annu. Rev. Immunol.

1,436

1,470

View full text Add to dashboard Cite

show abstract

“…These findings were extended in an electron tomography study of manually selected negatively-stained detergent-extracted full-length human αIIbβ3 bound to RGD peptide and imaged at 23 tilt angles. This study also revealed Hybrid domain swing-out in an extended integrin conformation, although it was not possible to determine if the conformation is linear, since the averages do not display density for the leg domains [32]. 2D projections of negativestained ectodomains from αA-lacking-or containing integrins showed images consistent with at least three conformations: a bent state and reportedly linear states without or with the Hybrid swing-out [23].…”

Section: Electron Microscopy (Em) Of Negatively Stained Ectodomain Anmentioning

confidence: 78%

“…The concentration of Mn 2+ used was sufficient however to form a stable ectodomain-ligand complex in solution, an accepted definition of the integrin high affinity state. Sample bias was excluded by using an automated selection routine, in addition to the manual selection used exclusively in the studies imaging complete ectodomains or full-length structures [23,28,32]. Model bias was inferred from the failure to observe density in the β-genu in the unliganded state (the β-genu was not included in the search model).…”

Section: Electron Microscopy (Em) Of Negatively Stained Ectodomain Anmentioning

confidence: 99%

Structure and mechanics of integrin-based cell adhesion

Arnaout

Xiong

2007

Current Opinion in Cell Biology

367

280

View full text Add to dashboard Cite

Summary of Recent AdvancesIntegrins are α/β heterodimeric adhesion glycoprotein receptors that regulate a wide variety of dynamic cellular processes such as cell migration, phagocytosis and growth and development. X-ray crystallography of the integrin ectodomain revealed its modular architecture and defined its metaldependent interaction with extracellular ligands. This interaction is regulated from inside the cell (inside-out activation), through the short cytoplasmic α and β integrin tails, which also mediate biochemical and mechanical signals transmitted to the cytoskeleton by the ligand-occupied integrins, which effect major changes in cell shape, behavior and fate. Recent advances in the structural elucidation of integrins and integrin binding cytoskeleton proteins are the subject of this review.

show abstract

“…The advantages of processing extracted per-particle subtiltseries rather than extracting subtomograms directly after reconstruction have been previously demonstrated (Iwasaki et al 2005;Zhang & Ren 2012;Bartesaghi et al 2012). In EMAN2, subtiltseries extraction from aligned tiltseries is automated through e2spt_subtilt.py, using the 3-D coordinates of subtomograms to geometrically estimate their position in each tilt image.…”

Section: Particle Picking: Subtomogram and Subtiltseries Extraction-thementioning

confidence: 99%

“…Of note, it has been suggested that direct Fourier inversion can produce more accurate 3-D reconstructions (Heymann et al 2008) than the more traditional WBP and SIRT (Radermacher 2006) methods used in the field. Furthermore, since gold fiducials are absent from tilt series in cases where they might interact with the specimen and, when present, they undergo beam-induced motion resulting in unavoidable errors in whole-frame alignment (Comolli, & Downing 2005), subtiltseries can allow for more accurate individual per particle alignment, refinement and reconstruction, provided that the data have enough contrast, as demonstrated for negatively stained data (Iwasaki et al 2005) and cryoET data (Zhang, & Ren 2012).…”

Section: Introductionmentioning

confidence: 99%

Single Particle Tomography in EMAN2

et al. 2012

View full text Add to dashboard Cite

Single particle tomography (SPT or subtomogram averaging) offers a powerful alternative to traditional 2-D single particle reconstruction for studying conformationally or compositionally heterogeneous macromolecules. It can also provide direct observation (without labeling or staining) of complexes inside cells at nanometer resolution. The development of computational methods and tools for SPT remains an area of active research. Here we present the EMAN2.1 SPT toolbox, which offers a full SPT processing pipeline, from particle picking to post-alignment analysis of subtomogram averages, automating most steps. Different algorithm combinations can be applied at each step, providing versatility and allowing for procedural cross-testing and specimen-specific strategies. Alignment methods include all-vs-all, binary tree, iterative singlemodel refinement, multiple-model refinement, and self-symmetry alignment. An efficient angular search, Graphic Processing Unit (GPU) acceleration and both threaded and distributed parallelism are provided to speed up processing. Finally, automated simulations, per particle reconstruction of subtiltseries, and per-particle Contrast Transfer Function (CTF) correction have been implemented. Processing examples using both real and simulated data are shown for several structures.

show abstract

Electron tomography reveals diverse conformations of integrin αIIbβ3 in the active state

Cited by 56 publications

References 31 publications

Structural Basis of Integrin Regulation and Signaling

Structural Basis of Integrin Regulation and Signaling

Structure and mechanics of integrin-based cell adhesion

Single Particle Tomography in EMAN2

Contact Info

Product

Resources

About