GBSN - Microbiology (Unit 3)Defense Mechanism of the body
Helical
1. An Introduction to Single Particle
Helical Reconstruction
Christos Gatsogiannis
31. January 2019
2. A wide range of biological assemblies are constructed from
subunits arranged in a regular manner.
two- or three-dimensional crystals, helices, or viruses.
3. each repeating unit is located in an equivalent environment (at least approximately)
the interactions between subunits are always the same
only a small number of interaction surfaces need to be specified
assemblies in which the units are equivalent require
much less information to specify their structure and can
easily self-assemble
12. Helices can be thought of as special cases of two-dimensional crystals, in which the
crystalline sheet has been deformed into a cylinder or a sphere, respectively.
Stewart,1988
14. How to determine handedness?
Milan and Eppickson, Journal Cell Biology, 1982
15. Filaments are thin elongated assemblies. The main subunit
interactions are found at the center of the filament and
between units above and below
Tubular assemblies often have wider helical radii than
filaments and possess a hollow center. The main interactions
are stabilized between adjacent units from all sides of the
helical lattice.
Sache, AIMS, 2015
16. azimuthal rotation angle Δφ
is the angle by which each subunit must be rotated to overlap
with its next copy (80° in the example shown)
axial rise Δz,
is the translation along the axis between subunits.
r
the outer radius of the cylinder that encompasses the filament
repeat,
is the distance that a subunit needs to be translated axially to b
in exact register with another subunit
Pitch
is the distance over which the helix makes a 360° turn.
(For the case illustrated the repeat is exactly 2 times the pitch
(4.5 subunits per pitch; 9 subunits per repeat).
Behrmann et al, J Struct Biol, 2012
19. CTER
CTER CTF Estimation
CTER CTF Assessment
Rapid Estimation of CTF parameters with error assessment
• CTER runs are indepedently repeated multiple times
• average and standard deviation are calculated for
each parameter
22. small segments can correct distortions
But decrease the alignment accuracy
During the segmentation, the approximate in-
plane angle of the particle axis is determined and
used to detect any erroneous alignment of
segments within the particle in later processing
steps
the step size will include approximately an integer
number of subunits (to 4) to be compatible with
the subsequent symmetrization
For example, an actin filament has a helical rise of
2.75 nm per subunit. Therefore, a step size of
min. 8.25 nm would be appropriate
Sachse et al., JMB, 2007
