8Q6J

Atomic structure and conformational variability of the HER2-Trastuzumab-Pertuzumab complex


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
experimental modelPDB 1N8Z 
experimental modelPDB 1S78 
experimental modelPDB 6OGE 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.134
f_angle_d0.702
f_chiral_restr0.046
f_bond_d0.007
f_plane_restr0.006
Sample
Ternary complex of her2-trastuzumab-pertuzumab Fabs
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles711008
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (1n8z, 1s78, 1s78, 6oge)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)60
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS GLACIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.1
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification240000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.2
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC4.1.2
MODEL FITTINGUCSF ChimeraX1.4
MODEL FITTINGPHENIX1.20.1
MODEL FITTINGCoot0.8.9.2
MODEL REFINEMENTPHENIX1.20.1
MODEL REFINEMENTCoot0.8.9.2
INITIAL EULER ASSIGNMENTcryoSPARC4.1.2
FINAL EULER ASSIGNMENTcryoSPARC4.1.2
CLASSIFICATIONcryoSPARC4.1.2
RECONSTRUCTIONcryoSPARC4.1.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2954825