8D4G | pdb_00008d4g

gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes

ELECTRON MICROSCOPY

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CM9
experimental model	PDB	4EN2

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.4789
f_angle_d	0.2784
f_chiral_restr	0.0635
f_plane_restr	0.0009
f_bond_d	0.0007

Sample
Complex of AP-1, Arf1, Nef and MHC-I cytosolic tail on a tubulated lipid bilayer
Sample Components
AP-1 heterotetramer

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.

3D Reconstruction
Reconstruction Method	SUBTOMOGRAM AVERAGING
Number of Particles	5094
Reported Resolution (Å)	11.6
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (6CM9, 4EN2, 4EN2)
Refinement Space
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	3

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	4500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	42000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
VOLUME SELECTION	Dynamo	1.1.532
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	NOVACTF
MODEL FITTING	UCSF Chimera	1.14
MODEL FITTING	UCSF ChimeraX	1.3
MODEL REFINEMENT	PHENIX	1.20-4459
RECONSTRUCTION	RELION	3.1.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING ONLY	CTF was estimated on a per-tilt basis in IMOD (4.11) using CTFPLOTTER. The results were used as input to NOVACTF during 3DCTF correction.