REL PDBe PDBe PDBe 2015-03-18 2015-04-01 2015-11-18 2015-11-25 Structural characterization of the Olfactomedin-1 disulfide-linked tetramer Sharp TH Pronker MF Bos TG Thies-Weesie DM Janssen BJC Olfactomedin-1 (Olfm1), neurobiology, tetramer, X-ray crystallography, small-angle X-ray scattering (SAXS), electron tomography, analytical ultracentrifugation (AUC), coiled coil, calcium, disulfide Pronker MF Bos TG Sharp TH Thies-Weesie DM Janssen BJC Olfactomedin-1 Has a V-shaped Disulfide-linked Tetrameric Structure J.BIOL.CHEM. 290 15092 15101 2015 25903135 doi:10.1074/jbc.M115.653485 Olfactomedin-1 disulfide-linked tetramer Olfactomedin-1 disulfide-linked tetramer Tetramer 1 0.242 0.256 AUC Olfactomedin-1
Purified recombinant full-length glycoslated Olfactomedin-1 tetramers were negatively stained with uranyl formate.
1 Tetramer IPR022082 IPR003112 true Mus musculus House Mouse brain neuron Secretory pathway Secreted (ER/golgi/extracellular) 0.242 0.256 Homo sapiens HEK293ES pUPE107.03 tomography particle 0.065 7.5
150 mM NaCl, 20 mM HEPES
 NEGATIVE
Full-length Olfm1 was adsorbed to grids for 30 sec. Grids were briefly washed with water and then stained for 30 sec with a freshly prepared filtered 2% uranyl formate solution.
Carbon-coated mesh copper grids glow discharged for 15 sec
 NONE OTHER FEI TECNAI F20 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2 2.0 2.0 30000.0 SIDE ENTRY, EUCENTRIC Objective lens astigmatism was corrected at 30,000 times magnification
Weak beam illumination
2015-02-12 GATAN ULTRASCAN 4000 (4k x 4k) 58 32. -58 58 2
Tilt series were collected from -58 to 58 degrees in 2 degree increments. The first and last image was discarded. CTF correction was performed on each projection
OTHER IMOD, EMAN2
Sub-tomogram particles were manually picked using e2spt_boxer.py from EMAN2. Each particle was normalized and masked with a sharp spherical mask to remove background density not associated with the protein. Particles were then filtered to 20 A with a low-pass Gaussian filter, before a tight mask was applied to the remaining density using e2proc3d.py from EMAN2.
57
IMOD, each tilt image
 emd_2943.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 100 100 100 -50 -50 -50 100 100 100 457.00003 457.00003 457.00003 90.0 90.0 90.0 X Y Z -3.83382893 5.40675211 0.01046992 0.19859882 4.57 4.57 4.57 1.0 AUTHOR Subtomogram of an Olfactomedin-1 tetramer
::::EMDATABANK.org::::EMD-2943::::
 5AMO A B RIGID BODY FIT Chimera
Each coiled-coil dimer of the tetramer was fitted as a rigid body.
REAL