3J4F

Structure of HIV-1 capsid protein by cryo-EM


ELECTRON MICROSCOPY
Sample
HIV-1 capsid protein
Specimen Preparation
Sample Aggregation StateHELICAL ARRAY
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsWith 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl, 50 mM Tris, pH 8.0) to back side. Blot 3-5 seconds from back side and plunge ...With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl, 50 mM Tris, pH 8.0) to back side. Blot 3-5 seconds from back side and plunge into liquid ethane with a homemade plunger.
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles3210
Reported Resolution (Å)8.6
Resolution MethodFSC 0.5 CUT-OFF
Other Details(Helical Details: The segments were aligned and reconstructed using Frealign. Twofold symmetry was imposed using IHRSR++.)
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise7.247
Angular Rotation31.13
Map-Model Fitting and Refinement
Id1 (2KOD)2 (3H47)
Refinement SpaceREALREAL
Refinement ProtocolFLEXIBLE FITFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsMETHOD--Seven hexamers were docked into density then solvated into 1M NaCl. Secondary structure restraints were applied to helices 1 to 11. MDFF was ...METHOD--Seven hexamers were docked into density then solvated into 1M NaCl. Secondary structure restraints were applied to helices 1 to 11. MDFF was run for 10 ns with symmetry restraints between CA monomers along the chiral axis. The center hexamer was then extracted. PDB entries 3H47 and 2KOD were the starting structures. REFINEMENT PROTOCOL--flexible
METHOD--Seven hexamers were docked into density then solvated into 1M NaCl. Secondary structure restraints were applied to helices 1 to 11. MDFF was ...METHOD--Seven hexamers were docked into density then solvated into 1M NaCl. Secondary structure restraints were applied to helices 1 to 11. MDFF was run for 10 ns with symmetry restraints between CA monomers along the chiral axis. The center hexamer was then extracted. PDB entries 3H47 and 2KOD were the starting structures. REFINEMENT PROTOCOL--flexible
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)15
Imaging Experiment1
Date of Experiment2010-12-11
Temperature (Kelvin)82
Microscope ModelFEI POLARA 300
Minimum Defocus (nm)1000
Maximum Defocus (nm)3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelOTHER
Nominal Magnification59000
Calibrated Magnification58257
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGMDFF
RECONSTRUCTIONFREALIGN
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
each filament