Cell Migration Gateway Logo

Structure - Activities

Objectives

  • functional integration in space and time for formulating atomic models of migration organelles
  • determine atomic resolution structures of each major protein involved in the organelle
  • one example of each class of domain:domain interaction

Structures | Algorithm Development

Structures Being Studied

Structure Method Status / Publication Contact (Collaborators)
Arp2/3 activation (mutants)
EM, single particle reconstruction and docking Completed - Martin et al., 2005 (CMC Update Article) Hanein (Drubin, Volkmann)
Arp2/3 branch structure
Cryo EM Data available - 2D structure Volkmann et al., 2001 Hanein (Volkmann, Li, Pollard)
2D crystallization on lipid monolayers Completed - Kelly et al., 2006 Taylor (Liddington)
2D crystallization on lipid monolayers Completed - Kelly and Taylor, 2005 (CMC Update Article) Taylor
Layilin-talin (196-400) PDB link
X-Ray crystallography, NMR Completed - Structure was solved by NMR Wegener et al., 2008 Liddington
PIPKIg -talin (196-400) PDB link
X-Ray crystallography, NMR Completed - de Pereda et al., 2005 (CMC Update Article) Liddington (Campbell)
Cryo EM, helical reconstruction, docking Completed - Volkmann and Hanein, 2000; Volkmann et al., 2000; Volkmann et al., 2003; Lowey et al., 2007; Trybus et al., 2007; Volkmann et al., 2007 Hanein (Volkmann, Lowey, Trybus, DeRosier)
Actin fimbrin crosslink PDB link
EM and bioinformatics Data available - Volkmann et al., 2001 Hanein (Volkmann)
Actin comet tail
Correlative light microscopy-electron microscopy Completed - Cameron et al., 2001 Borisy (Theriot)
Actin filaments orientational order in vivo
Correlative light microscopy-electron microscopy Completed - Verkhovsky et al., 2003 Borisy (Meister)
F-actin-villin (with David DeRosier)
Electron Tomography Completed - Hampton et al., 2008 (CMC Update Article) Taylor (DeRosier)
Talin (Ferm-domain) and Actin
EM and helical reconstruction Completed - Lee et al., 2004 Hanein (Liddington, Critchley, Volkmann)
Tensin SH2 and PTB domains PDB link
X-Ray crystallography, NMR Completed - McCleverty et al., 2007 (CMC Update Article) Liddington
Tropomyosin and the leading edge
conventional EM Completed - Gupton et al., 2005 (CMC Update Article) Hanein (Waterman-Storer)
Meta-vinculin C-terminal domain PDB link
X-Ray crystallography, NMR Completed - Bakolitsa et al., 1999 Liddington
Vinculin (full length) PDB link
X-Ray crystallography Data available - Bakolitsa et al., 1999; Bakolitsa et al., 2004 (CMC Update Article); Saunders et al., 2006; Ziegler et al., 2006 (CMC Update Article) Liddington
EM, tomography and docking Completed - Janssen et al., 2006 (CMC Update Article) Hanein (Volkmann, Liddington)
WASP and Scar - Drosophila actin nucleation
Correlative light microscopy-electron microscopy Completed - Biyasheva et al., 2004 Borisy (Baum)
Alpha-actinin cross-links
2D crystallization on lipid monolayers Completed - Hampton et al., 2007 (CMC Update Article) Taylor
Alpha-actinin2 (chicken smooth muscle) PDB link
2D crystallization on lipid monolayers Completed - Liu et al., 2004 Taylor (Liu)
X-Ray crystallography, NMR Data available - Hayashi et al., 2002 Liddington
HIV-cytoskeletal association (microtubules)
Correlative light microscopy-electron microscopy Completed - McDonald et al., 2002 Borisy (Hope)
Lamellipodia leading edge (Ena/VASP) proteins
Correlative light microscopy-electron microscopy Completed - Bear et al., 2002 Borisy (Gertler)

alphaIIb-beta3 integrin structure in the membrane

PDB link

Electron Tomography

Completed - Ye et al., 2008 (CMC Update Article) Taylor

Alpha-actinin / beta1-integrin - vinculin 1-258 - talin FERM domain complex

PDB link

2D crystallization on lipid monolayers

Completed Taylor (Liddington)

X-Ray crystallography

Completed Liddington

X-Ray crystallography

Completed Liddington

Fibronectin fibrillogenises

PDB link

EM, light and EM labeling, cell culture

Completed Hanein (Geiger, Engel, Ruoslahti)

Fibronectin structure

PDB link

EM, Cryo EM and tomography

Completed Hanein (Volkmann, Engel)

GIT-1 domains

PDB link

X-Ray crystallography

Completed - subcloning and expression Liddington

X-Ray crystallography

Completed - protein expressed and purification for crystal trials Liddington

EM and biochemistry

Completed Hanein (Higgs)

NMR

Completed Campbell (Ginsberg)

Fimbrin - actin regulation

PDB link

EM and biochemistry

Completed Hanein (Volkmann)

X-Ray crystallography

Completed - protein expressed and purification for crystal trials Liddington

Paxillin (1-328)-FAT domain of FAK

PDB link

NMR

Completed Campbell

Paxillin -wt fragments 1-328 & 325-557 and full-length

PDB link

X-Ray crystallography

Completed Liddington

Actin networks

PDB link

VMP, Cryo EM and tomography

Completed Hanein (Volkmann)

X-Ray crystallography, NMR

Data available - crystallized and solved GarcĂ­a-Alvarez et al., 2003; Wegener et al., 2007 (CMC Update Article); Calderwood et al., 2013 Liddington (Campbell, Ginsberg)

2D crystallization on lipid monolayers

Completed Taylor

Talin C-terminal actin binding site (I/LWEQ motif)

PDB link

NMR

Completed - Gingras et al., 2009; Goult et al., 2009 (CMC Update Article) Critchley

Talin (C-terminal Actin-binding domain)

PDB link

EM, SAXS, docking and helical reconstruction

Completed - Gingras et al., 2008 (CMC Update Article); Bate et al., 2012 (CMC Update Article); Goult et al., 2013 (CMC Update Article); Goult et al., 2013 (CMC Update Article) Hanein (Liddington, Critchley, Volkmann)

Talin C-terminal helix required for dimer formation

PDB link

X-Ray crystallography

Completed - Gingras et al., 2008 (CMC Update Article); Gingras et al., 2009 Critchley

Talin FO/F1(1-200)

PDB link

NMR

Completed - Gingras et al., 2008 (CMC Update Article) Critchley

Talin fragments for protein splicing and chemical labeling

PDB link

Cell-based studies

Completed Liddington

Talin (full length)

PDB link

X-Ray crystallography

Completed Liddington

Talin head for head-tail binding studies

PDB link

Calorimetric

Completed Liddington

2D crystallization on lipid monolayers

Completed Taylor (Liddington)

Talin rod 655-911

PDB link

NMR

Completed - Patel et al., 2006 Critchley

Talin-rod domain and actin

PDB link

EM and helical reconstruction

Completed Hanein (Liddington)

X-Ray crystallography

Completed - Patel et al., 2006 Liddington

EM, tomography, single particle reconstruction, and bioinformatics

Completed Hanein (Gertler, Volkmann)

Metavinculin (fragments and full length)

PDB link

X-Ray crystallography, NMR

Completed - Crystalization trials - residues 879-1134; metavinculin residues 895-11; full-length metavinculin Liddington

Vinculin and Arp2/3 complex formation

PDB link

X-Ray crystallography

Completed Liddington

Atomic Force Microscope

Completed Liddington

Vinculin N-terminal domain complex with alpha-actinin1 domain 3

PDB link

X-Ray crystallography

Completed - complex purification and crystallization trials Liddington

Electron Tomography

Completed - Collins et al., 2011 (CMC Update Article) Taylor

2D crystallization on lipid monolayers

Completed Taylor

Alpha-actinin1 (plus calcium)

PDB link

2D crystallization on lipid monolayers

Completed Taylor

lipid monolayer, negative stain, single particle image processing

Completed - Hampton et al., 2007 (CMC Update Article) Taylor

Beta tails as an interaction hub

PDB link

NMR

Completed - Competition between PTB domains of talin, Dok1, ICap-1, effect of phosphorylation. Oxley et al., 2008 (CMC Update Article) Campbell

Cell-matrix interactions

PDB link

Multi color labeling

Completed - Luxenburg et al., 2007 (CMC Update Article); Zamir et al., 2008 (CMC Update Article) Geiger (Hanein)

Crawling cells (with Condeelis)

PDB link

Electron Tomography

Completed Taylor (Condeelis)

C-terminal fragment of Tensin and actin

PDB link
Completed - McCleverty et al., 2007 (CMC Update Article); Leone et al., 2008 (CMC Update Article) Hanein (Li, Li, Vuori, Volkmann, Liddington)

Focal adhesion structure in-situ

PDB link

VMP, light and EM, labeling, Cryo EM and tomography

Completed Hanein (Geiger)

Focal adhesion structure

PDB link

Correlative light microscopy-electron microscopy

Completed - Hanein and Volkmann, 2011 Geiger (Hanein)

Full-length FAK

PDB link

X-Ray crystallography

Completed - Protein expressed and purification for crystal trials Liddington

Full-length talin and actin

PDB link

EM and tomography

Completed - Goult et al., 2013 (CMC Update Article) Hanein (Volkmann, Liddington)

Full-length tensin and actin

PDB link

Cryo EM

Completed Hanein (Vuori)

Full-length Vinculin actin

PDB link

EM, tomography, single particle reconstructions, docking

Completed Hanein (Volkmann, Liddington)

Isolated membrane protrusions (with Klemke)

PDB link

Electron Tomography

Completed Taylor (Klemke)

Leading edge

PDB link

VMP, Cryo EM and conventional EM

Completed Hanein

Mapping of molecular sub-domains

PDB link

Multi color labeling; Clustering analysis

Completed - Zamir et al., 2008 (CMC Update Article); Geiger and Yamada, 2011 Geiger
Podosome structure
VMP and Cryo EM Completed - Geblinger et al., 2009 (CMC Update Article) Geiger (Hanein)

Organization of zyxin and alpha-actinin in focal adhesions and stress fibers

PDB link

Correlative light microscopy-electron microscopy

Completed Geiger (Hanein)

Organization of zyxin and alpha-actinin in focal adhesions and stress fibers

PDB link

Correlative light microscopy-electron microscopy

Completed Geiger (Hanein, Taylor)

Osteoclast structure

PDB link

Multi color labeling

Completed - Luxenburg et al., 2007 (CMC Update Article); Anderegg et al., 2011; Geblinger et al., 2011 (CMC Update Article) Geiger

PIP3 binding DHR1 domain of DOCK180

PDB link

X-Ray crystallography

Completed Liddington (Vuori, Cote)

Podosome structure

PDB link

Correlative light microscopy-electron microscopy

Completed - Luxenburg et al., 2007 (CMC Update Article); Geblinger et al., 2009 (CMC Update Article); Luxenburg et al., 2012 (CMC Update Article) Geiger (Hanein)
Rickettsia - structure of tail mediated by WASP-like protein
Correlative light microscopy-electron microscopy Completed - Jeng et al., 2004 Borisy (Welch)
return to top


Algorithm Development and Refinement

Algorithm & Application Status / Publication Contact (Collaborators)
Adaptation of watershed transform for use with light microscopy Completed Volkmann (Hanein, Danuser, Waterman, Geiger)
Application of docking algorithms for high-resolution interpretation of cryoEM maps Completed - Lee et al., 2004; Janssen et al., 2006 (CMC Update Article); Lowey et al., 2007; Trybus et al., 2007; Gingras et al., 2008 (CMC Update Article); Rouiller et al., 2008 (CMC Update Article) Volkmann (Hanein, Liddington, Critchley)
Application of filament tracking approaches to interpretation of worm sperm tomograms Completed Volkmann (Taylor, Roberts)
Averaging of motifs extracted from tomographic reconstructions Completed - Technical publication in preparation Rouiller et al., 2008, first published application (CMC Update Article) Volkmann
Improved single-particle reconstruction algorithms for small particles and mixed populations Completed Volkmann
Refinement of docking algorithms for high-resolution interpretation of cryoEM maps Completed - Volkmann and Hanein, 2003; Shacham et al., 2007 Volkmann
Refinement of docking algorithms for use with tomograms Completed - software available, technical publication in preparation Rouiller et al., 2008 (CMC Update Article) Volkmann (Hanein)
Refinement of reconstruction algorithms for helical structures Completed - Janssen et al., 2006 (CMC Update Article); Lowey et al., 2007; Trybus et al., 2007; van der Heide et al., 2007 (CMC Update Article); Gingras et al., 2008 (CMC Update Article) Volkmann
Refinement of watershed segmentation for use with electron tomograms Completed - Volkmann, 2002 Volkmann (Hanein, Taylor, Marsh)
Test and refinement of noise reduction algorithms for tomographic reconstructions Completed - van der Heide et al., 2007 (CMC Update Article) Volkmann (Hanein, Taylor, Marsh)
Test and refinement of reduced-representation templates for filament detection in electron tomograms Completed Volkmann (Hanein, Taylor)
Use of reduced-representation templates for particle selection in cryoEM Completed - Volkmann, 2004 Volkmann

The 3D watershed transform (Volkmann, 2002) has been successfully adapted and applied to time series data from light microscopy (with Hanein, Danuser and Waterman). The computer programs and parameter sets developed and refined in connection with this project are available upon request.


return to top