6NZ0

Cryo-EM structure of AAV-2 in complex with AAVR PKD domains 1 and 2

ELECTRON MICROSCOPY

Sample
Adeno-associated virus - 2
Sample Components
Binary complex of AAV-2 with a fragment of its cellular receptor, AAVR or dyslexia-associated protein KIAA0319-like protein.

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	4ul of AAV-2 (1.7uM) was added to the grid, followed by 4ul of AAVR-PKD1-2 (16.7uM), with manual blotting after each addition with Whatman paper (Cat. ...	4ul of AAV-2 (1.7uM) was added to the grid, followed by 4ul of AAVR-PKD1-2 (16.7uM), with manual blotting after each addition with Whatman paper (Cat. no. 1001-110.) 4ul of buffer containing 25mM HEPES, 150mM NaCl, pH 7.4 was added to the grid before final blotting and plunge-freezing in the Vitrobot (blot time 1.5sec, blot force -1).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	21373
Reported Resolution (Å)	2.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1LP3)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Map values at grid points within 2 Angstrom of atoms
Overall B Value
Fitting Procedure
Details	An initial model for AAVR was constructed by homology modeling using Modeller 9.2. After remodeling AAVR and the crystal structure of AAV2, the struc ...	An initial model for AAVR was constructed by homology modeling using Modeller 9.2. After remodeling AAVR and the crystal structure of AAV2, the structure was refined using RSRef embedded in CNS for stereochemically restrained torsion angle simulated annealing and gradient descent optimization. Stand-alone RSRef was used for refinement of EM envelope corrections, resolution estimates, and restrained atomic B-factors.

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	25.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	-800
Maximum Defocus (nm)	-2000
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	75000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	3.0b
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	Gctf	1.06
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	RELION	3.0b
FINAL EULER ASSIGNMENT	RELION	3.0b
CLASSIFICATION	RELION	3.0b
RECONSTRUCTION	RELION	3.0b
MODEL REFINEMENT	RSRef

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		34450	RELION Autopicker using 3D AAV-2 reference filtered to 20A with 15 degree sampling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.