REL PDBe PDBe PDBe 2014-01-02 2014-01-15 2014-01-15 2014-04-23 Single particle electron cryomicroscopy of the complex between the E.coli enzyme beta-galactosidase and the single chain Fv antibody scFv13R4. Vinothkumar KR McMullan G Henderson R beta-galactosidase, antibody, scFv13R4, single particle cryoEM Vinothkumar KR McMullan G Henderson R Molecular mechanism of antibody-mediated activation of beta-galactosidase STRUCTURE 22 621 627 2014 24613486 doi:10.1016/j.str.2014.01.011 4ckd FULLOVERLAP Single chain Fv antibody domain bound to the enzyme beta-galactosidase Single chain Fv antibody domain bound to the enzyme beta-galactosidase
The occupancy of the antibody domains was estimated to be 90%
one D2 symmetry tetramer, with 4 Fv antibody domains (heavy & light chains) 3 0.560 Known stoichiometry and known molecular weights of the components, which are 450 kiloDaltons for the D2 beta-galactosidase and 28 kiloDaltons for each Fv domain. beta-galactosidase Escherichia coli K-12 0.465
Central tetrameric enzyme in complex
4 tetramer true P00722 GO:0009341 IPR001360 SCFV13R4 ANTIBODY FV HEAVY CHAIN Mus musculus HOUSE MOUSE 4 Tetrameric true Escherichia coli BL21(DE3) pet16B SCFV13R4 ANTIBODY FV LIGHT CHAIN Mus musculus HOUSE MOUSE 4 Tetrameric true Escherichia coli BL21(DE3) pet16b singleParticle particle 0.9 7.4
20% phosphate buffered saline (PBS)
 NEGATIVE
Sample applied to glow-discharged (30 seconds in residual air) grids, blotted and frozen rapidly in an environmental plunge-freeze apparatus (Bellare et al, J. Electr. Micros. Tech., 1988, 10, 87-111).
Qunatifoil grids with 1.2 micron holes
 ETHANE 100 100 OTHER Blot for 10-20 seconds until diameter of blotted meniscus ceases to expand, before plunging. FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.0 2.678 4.027 59000.0 81600.0 OTHER 88 90 89 Corrected at 200,000x once at start of session 0
Exposure intensity set to give 50 electrons/pixel/second at the detector. This translates into 16 electron/square_Angstrom/second at the specimen.
2012-08-02 FEI FALCON II (4k x 4k) 14 49 67
Every image is the average of all frames recorded by the Falcon II direct electron detector
16. Polara cartridges
The map was obtained using Frealign, with a starting model consisting of a similar map from 43,000 single particle images of beta-galactosidase without antibody.
done inside FREALIGN
 D2 OTHER 13.0 OTHER MRC, CTFFIND3, FREALIGN
Map was calculated from a single dataset of 2965 particles.
2965
as determined by FREALIGN. Orientations were determined using the data out to a resolution limited to 14 Angstroms
 emd_2548.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 100 100 100 0 0 0 100 100 100 300.0 300.0 300.0 90.0 90.0 90.0 X Y Z -0.05654818 0.32245788 -0.00343177 0.04594183 3.0 3.0 3.0 0.13 AUTHOR Map of the structure of the complex between beta-galactosidase and the scFv13R4 single chain antibody domain.
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 1F4A A B C D RIGID BODY FIT Chimera
Since there are three orthogonal two-fold axes, there are actually no parameters required for the fitting, except to make sure the three axes are correctly assigned (which they were at an earlier stage) and relative magnification, which was tested from 0.95 to 1.05, determined. In this case, at this resolution, a relative magnification of 1.00 was adequate. For the higher resolution map of beta-galactosidase without antibody, a 2.5% correction was necessary. In addition to 1F4A, we also fitted the coordinates of Fv antibody HYHEL-10 (anti-hen egg lysozyme) with PDB coordinates 3A6B to all four antibody domains in the map.
FSC curve between map and model REAL 0.0
emd_2548.tif