9FJF | pdb_00009fjf

Lysosomal transporting complex of beta-glucocerebrosidase (GCase) and lysosomal integral membrane protein 2 (LIMP-2) with bound Pro-macrobodies (Combined focus map)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TN1
experimental model	PDB	4Q4F
experimental model	PDB	9ENA

Sample
Lysosomal transporting complex of beta-glucocerebrosidase and lysosomal integral membrane protein 2 (LIMP-2) with two bound Pro-macrobodies.

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	397385
Reported Resolution (Å)	3.7
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6TN1)	2 (4Q4F)	3 (9ENA)
Refinement Space	REAL	REAL	REAL
Refinement Protocol	FLEXIBLE FIT	FLEXIBLE FIT	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Initial fitting with ChimeraX, manual flexible fitting with Coot, refinement with Phenix	Initial fitting with ChimeraX, manual flexible fitting with Coot, refinement with Phenix	Initial fitting with ChimeraX, manual flexible fitting with Coot, refinement with Phenix

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS GLACIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.2
IMAGE ACQUISITION	EPU
MASKING	UCSF ChimeraX	1.7.1
MASKING	cryoSPARC	4.2
CTF CORRECTION	cryoSPARC	4.2
MODEL FITTING	Coot	WinCoot 0.9.8.7
MODEL FITTING	UCSF ChimeraX	1.7.1
MODEL REFINEMENT	PHENIX
OTHER	MODELLER
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487
MODEL FITTING	Coot	WinCoot 0.9.8.7
MODEL FITTING	UCSF ChimeraX	1.7.1
MODEL REFINEMENT	PHENIX	1.20.1_4487
MODEL FITTING	Coot	WinCoot 0.9.8.7
MODEL FITTING	UCSF ChimeraX	1.7.1
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	PHENIX	1.20.1_4487

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.