Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a
Sample Components
human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG)
Ras-related protein Rab-5A
Specimen Preparation
Sample Aggregation State
3D ARRAY
Vitrification Instrument
FEI VITROBOT MARK I
Cryogen Name
ETHANE
Sample Vitrification Details
Blot force 20, blot time 6 s
3D Reconstruction
Reconstruction Method
SUBTOMOGRAM AVERAGING
Number of Particles
26979
Reported Resolution (Å)
9.8
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (5DFZ, 3MJH, 4DDP, 3IHY)
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
correlation
Overall B Value
320
Fitting Procedure
Details
An initial model was build with SWISSMODEL. using 5DFZ, 4DDP and 3IHY. This was then fit manually to density while running restrained MD with ISOLDE. ...
An initial model was build with SWISSMODEL. using 5DFZ, 4DDP and 3IHY. This was then fit manually to density while running restrained MD with ISOLDE. The model was refined in REFMAC with self-restraints (4.3) and restraints to 3MJH, 4DDP and 3IHY.