4V3M | pdb_00004v3m

Membrane bound pleurotolysin prepore (TMH2 helix lock) trapped with engineered disulphide cross-link


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OEB 
Sample
PLEUROTOLYSIN PREPORE ON LIPOSOMES (TMH2 HELIX LOCK) TRAPPED WITH ENGINEERED DISULPHIDE
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification DetailsVITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 80,INSTRUMENT- FEI VITROBOT MARK III, METHOD- PLEUROTOLYSIN A WAS FIRST ADDED TO SPHINGOMYELIN-CHOLESTER ...VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 80,INSTRUMENT- FEI VITROBOT MARK III, METHOD- PLEUROTOLYSIN A WAS FIRST ADDED TO SPHINGOMYELIN-CHOLESTEROL LIPOSOMES AT A MOLAR RATIO OF 1 TO 2000 ROTEIN TO LIPID IN THE ABOVE BUFFER. AFTER 5 MIN INCUBATION AT ROOM TEMPERATURE,PLEUROTOLYSIN B WAS ADDED TO THE MIXTURE AT A MOLAR RATIO OF 1 TO 2 TO PLEUROTOLYSIN A. THE MIXTURE WAS INCUBATED AT 40 C OR ROOM TEMPERATURE FOR 30 MIN AFTER WHICH 3.5 UL WERE PLACED ON NEGATIVELY GLOW DISCHARGED LACEY GRIDS AND VITRIFIED IN LIQUID ETHANE USING A VITROBOT. BLOTTING WAS CARRIED OUT AT 36 C AND 80 PERCENT HUMIDITY.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles722
Reported Resolution (Å)17
Resolution Method
Other DetailsUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2795. (DEPOSITION ID: 12858).
Refinement Type
Symmetry TypePOINT
Point SymmetryC13
Map-Model Fitting and Refinement
Id1 (4OEB)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCross-correlation coefficient
Overall B Value
Fitting Procedure
DetailsMETHOD--RIGID BODY
Data Acquisition
Detector TypeGATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)25
Imaging Experiment1
Date of Experiment2013-01-30
Temperature (Kelvin)94
Microscope ModelFEI POLARA 300
Minimum Defocus (nm)700
Maximum Defocus (nm)3700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.3
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification59000
Calibrated Magnification76148
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGFlex-EM
MODEL FITTINGMODELLER
MODEL FITTINGTEMPy
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONIMAGIC
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
ESTIMATED WITH CTFFIND3, THEN PHASES FLIPPED FOR EACH PARTICLE