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Structure of tetrameric HIV-1 Strand Transfer Complex Intasome
ELECTRON MICROSCOPY
Sample
complex formed by a tetrameric assembly of Sso7d-fusion HIV-1 Integrase with the product of DNA strand transfer
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
Sample containing HIV STC intasomes in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey gold UltrAuF ...
Sample containing HIV STC intasomes in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey gold UltrAuFoil grids (Quantifoil), adsorbed for 30 seconds, then plunged into liquid ethane using a manual cryo-plunger in an ambient environment of 4 degrees C.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
83766
Reported Resolution (Å)
3.9
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Resolution-limited refinement used throughout
Refinement Type
Symmetry Type
POINT
Point Symmetry
C2
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
FSC 0.5
Overall B Value
180
Fitting Procedure
Details
To generate ensemble models, the complete intasome model was iteratively relaxed - using two-fold symmetry and a combination of Rosetta and Phenix - a ...
To generate ensemble models, the complete intasome model was iteratively relaxed - using two-fold symmetry and a combination of Rosetta and Phenix - against one half map (the working map) and inspected for consistency with the second half map (the free map). The model was then adjusted manually using Coot. Final ensemble modeling used half maps for all aspects of refinement and evaluation: 500 models were generated as described using Rosetta. From the 100 top-scoring models (scored by Rosetta energy), the ten models with the best map-to-model FSC were selected and refined in real space using secondary-structure restraints in Phenix. Molprobity was used throughout the refinement process.