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 9BW6 | pdb_00009bw6

Human Vault Cage in complex with PARP4


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V60 
in silico modelAlphaFoldQ9UKK3 
Sample
Binary complex of human PARP4 bound to oligomerized human MVP
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsVitrification carried out under standard conditions
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles44443
Reported Resolution (Å)2.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryD39
Map-Model Fitting and Refinement
Id1 (4V60)2
Refinement SpaceREALREAL
Refinement ProtocolFLEXIBLE FITFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsThe starting model was the rat homologue of MVP from a previous crystal structure of the vault cage (PDB accession no 4V60). The final model was refin ...The starting model was the rat homologue of MVP from a previous crystal structure of the vault cage (PDB accession no 4V60). The final model was refined in real space and validated using PHENIX.
PARP4's MINT domain, predicted by AlphaFold2, was used as the starting model. The final model was refined in real space and validated using PHENIX.
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)45
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)700
Maximum Defocus (nm)1700
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.01
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification53000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsPreliminary grid screening was performed manually.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.4
IMAGE ACQUISITIONSerialEM4.0
CTF CORRECTIONcryoSPARC4.4
MODEL FITTINGCoot0.8.9.2
MODEL REFINEMENTPHENIX1.12
MODEL FITTINGCoot0.8.9.2
MODEL REFINEMENTPHENIX1.12
INITIAL EULER ASSIGNMENTcryoSPARC4.4
FINAL EULER ASSIGNMENTcryoSPARC4.4
CLASSIFICATIONcryoSPARC4.4
RECONSTRUCTIONcryoSPARC4.4
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF correction was performed when movies were imported into cryoSPARC Live670079