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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9RTW
pdb_00009rtw
10.2210/pdb9rtw/pdb
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FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Mammalian AP-3 complex assembled on tubular membranes
Specimen Preperation
Sample Aggregation State
HELICAL ARRAY
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE-PROPANE
Sample Vitrification Details
?
3D Reconstruction
Reconstruction Method
SUBTOMOGRAM AVERAGING
Number of Particles
42469
Reported Resolution (Å)
7.4
Resolution Method
FSC 0.143 CUT-OFF
Other Details
?
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
Alphafold 3 (AF3), was used to generate 5 models of mammalian AP3 in complex with two copies of ARF1 in the GTP bound conformation. As the structure from STA was in a much more extended conformation than AF3 models or previous structures, direct rigid body docking of the complete AF3 model into the STA density was not possible. To create the C1 model the predicted complex was separated into three submodels, each of which was independently fitted into the map as a rigid body. Submodel 1 consisted of sigma3 (1-193), delta (1-387), delta-ARF1 (1-181). Submodel 2 consisted of mu3 (1-418), beta3 (1-472), beta3-ARF1. Submodel 3 consisted of beta3 (473-636) and delta (388-638) formed submodel 3. Rigid body fitting was performed using ChimeraX. This positioned truncated regions of submodels 1 and 2 in close proximity to their adjoining regions in submodel3, thus the split beta3 and delta chains were rejoined into single chains before real-space refinement in COOT to correct bond angles, distances and torsions. Using the previously resolved ARF1 dimer (PDBID: 9C5A), ARF1 was first superimposed with the existing ARF1 on beta3 and delta before rigid docking into the EM density. Flexible regions not accounted for sufficiently by modellable density were removed, these regions are listed as follows; beta3 (1-42), beta3 (259-292), delta (1-17), sigma3 (154-193) and ARF1 (1-13). Side chains and rotamers were not modelled and were therefore removed in ChimeraX.
Data Acquisition
Detector Type
TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å
2
)
3
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
3000
Maximum Defocus (nm)
6000
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
?
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
?
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
VOLUME SELECTION
UCSF Chimera
?
VOLUME SELECTION
subTOM
?
VOLUME SELECTION
Warp
?
VOLUME SELECTION
M
?
VOLUME SELECTION
RELION
?
CTF CORRECTION
Warp
?
MODEL FITTING
UCSF ChimeraX
?
FINAL EULER ASSIGNMENT
RELION
?
CLASSIFICATION
RELION
?
RECONSTRUCTION
RELION
?
MODEL REFINEMENT
Coot
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
3DCTF in WARP
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