The pore structure of pneumolysin, obtained by fitting the alpha carbon trace of perfringolysin O into a cryo-EM map
ELECTRON MICROSCOPY
Sample
PNEUMOLYSIN
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
PLUNGED INTO ETHANE
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
88
Reported Resolution (Å)
29
Resolution Method
Other Details
RESIDUES 134-142 ARE MISSING FROM THE SEQUENCE. RESIDUES CORRESPONDING TO TO TM1 AND TM2 (187-220,284-315) WERE MODELLED AS A POLY-ALANINE FLAT BETA H ...
RESIDUES 134-142 ARE MISSING FROM THE SEQUENCE. RESIDUES CORRESPONDING TO TO TM1 AND TM2 (187-220,284-315) WERE MODELLED AS A POLY-ALANINE FLAT BETA HAIRPINS. THE OLIGOMER CAN BE GENERATED BY APPLYING 38-FOLD ROTATIONAL SYMMETRY.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C38
Map-Model Fitting and Refinement
Id
1 (1PFO)
Refinement Space
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
METHOD--THE CRYSTAL STRUCTURE OF PERFRINOGLYSIN O (1PFO, ROSSJOHN ET AL., 1998,
CELL 89, 685)WAS PLACED INTO THE CRYO-EM DENSITY MAP (EMD-1107). THE ...
METHOD--THE CRYSTAL STRUCTURE OF PERFRINOGLYSIN O (1PFO, ROSSJOHN ET AL., 1998,
CELL 89, 685)WAS PLACED INTO THE CRYO-EM DENSITY MAP (EMD-1107). THE ALPHA
CARBON TRACE OF PERFRINGOLYSIN 0 WAS MANUALLY POSITIONED INTO THE CRYO-EM
DENSITY CORRESPONDING TO THE POSITION OF ONE SUBUNIT. THE BEST FIT WAS OBTAINED
BY SEPARATING THE MONOMER INTO SIX RIGID BODIES- DOMAIN 1(91-172, 231-272
354-373), DOMAIN 2 UPPER (53- 62, 83-90, 374-381), DOMAIN 2 LOWER (63-82,
382-390), DOMAIN 3 (177-186, 221-230, 273-283, 316-353), DOMAIN 3 HAIRPINS
(187- 220, 284-315), AND DOMAIN 4 (391-500). THE COMPLETE OLIGOMER (38-MER) WAS
GENERATED AND CHECKED FOR CLOSE CONTACTS BOTH BY EYE AND USING THE CCP4 PROGRAM
CONTACT.TO IMPROVE THE FIT SECTIONS CORRESPONDING TO 3 SUBUNITS WERE EXTRACTED
FROM THE 38-MER MAP (EMD-1107) AND A 44-MER MAP AND ALIGNED. THE WEIGHTED
AVERAGE WAS CALCULATED AND THE IMPROVED MAP USED FOR THE FINAL MANUAL FITTING.
THE TWO SECTIONS ARE CONSISTENT TO A RESOLUTION OF 28 ANGSTROMS (0.5
CORRELATION FSC) AND THE WEIGHTED AVERAGE MAP WAS RECONSTRUCTED FROM 131
PARTICLES.
Data Acquisition
Detector Type
KODAK SO-163 FILM
Electron Dose (electrons/Å**2)
20
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
100
Microscope Model
FEI TECNAI F20
Minimum Defocus (nm)
1100
Maximum Defocus (nm)
3200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
42000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
