2024-03-06 REL RCSB RCSB RCSB 2020-10-14 2020-12-16 2020-12-16 2024-03-06 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM122564 United States Adeno-Associated Virus (AAV-DJ) - cryo-EM structure at 1.56 Angstrom Resolution Xie Q Yoshioka CK Gene therapy vector, VIRUS LIKE PARTICLE, VIRUS Xie Q Yoshioka CK Chapman MS Adeno-Associated Virus (AAV-DJ)-Cryo-EM Structure at 1.56 Angstroms Resolution. Viruses CH 12 2020 33092282 doi:10.3390/v12101194 1999-4915 7kfr FULLOVERLAP Adeno-associated virus Adeno-associated virus 0 1 Adeno-associated virus Homo sapiens 3.746 250.0 1 VIRUS-LIKE PARTICLE STRAIN false true Capsid protein VP1 Adeno-associated virus 0.058877808999999996 1 Spodoptera frugiperda LEVO GADGVGNSSGNWHCDSTWMGDRVITTSTRTWALPTYNNHLYKQISNSTSGGSSNDNAYFGYSTPWGYFDFNRFHCHFSPR DWQRLINNNWGFRPKRLSFKLFNIQVKEVTQNEGTKTIANNLTSTIQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMIPQ YGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFQFTYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTQTTGGT TNTQTLGFSQGGPNTMANQAKNWLPGPCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFF PQSGVLIFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGVLPGMVWQDRDVYLQ GPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPADPPTTFNQSKLNSFITQYSTGQVSVEIEWELQKENSKRW NPEIQYTSNYYKSTSVDFAVNTEGVYSEPRPIGTRYLTRNL Q6JC41 MAGNESIUM ION 2.4305e-05 3 MG water 1.8015e-05 265 HOH singleParticle particle 0.6 7.4 50.0 HEPES 25.0 MgCl2 Magnesium chloride 25.0 NaCl Sodium chloride Quantifoil COPPER 200 GLOW DISCHARGE OTHER 0.03
PELCO easiGlow Glow Discharge Cleaning System Current: 15mA
 ETHANE 100 293 FEI VITROBOT MARK IV
Two 3uL aliquots applied to grid (manual blotting between), prior to automated 3 second blot before plunging..
Monodisperse
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 -0.8 -2.6 155000.0 154400.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 93.0 93.0
Coma-free alignment and objective astigmatism where corrected using Sherpa (Thermo Fisher, Inc.).
FEI FALCON III (4k x 4k) INTEGRATING 4096 4096 1 2241 15.8 30.0
Data were collected with pixel size of 0.514 angstrom on a FEI Titan Krios (Thermo Fisher, Inc.) at 300 kV, using a Falcon 3 camera (Thermo Fisher) with a total dose of approx. 30 e-/A2 fractionated across 200 frames. Camera dose rate was approx. 0.5 e-/pixel/s. Defocus was random in the nominal range of -0.8 to -2.6 um. Images were acquired in EPU (Thermo Fisher, Inc.) without using image shift.
 1 75316
DoG (Difference of Gaussian) Picker was used for initial automated particle selection. Templates were then generated by 2D classification, followed by particle template selection in Relion 3.0.
 1 I 1.56 FSC 0.143 CUT-OFF RELION 3.0
These 48209 particles refined to approx. 2.2 A with I1 symmetry, and subsequent refinements of beam tilt and per-particle CTF brought the resolution to 1.8 A. Further particle-polishing and subsequent re-refinement of CTF brought the resolution to 1.70 A and a final reconstruction using Ewald sphere correction ended at 1.56 A. The map used for modeling was sharpened using the volume whitening routine in cisTEM.
48209 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 RELION 3.0
Multiple rounds of 2D classification and 3D classification with C1 symmetry were used to remove outliers, resulting in 48,209 particles after deduplication.
 emd_22854.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 -300 -300 -300 600 600 600 306.30002 306.30002 306.30002 90.0 90.0 90.0 Y X Z -0.177237 0.372257 -0.000013357471 0.017671466 0.5105 0.5105 0.5105 0.064 EMDB Full particle Relion map, sharpened using volume-whitening routine of cisTEM. Cropped version also provided for ease of comparison with coordinates. 5UF6 PDB experimental model FLEXIBLE FIT
Stand-alone RSRef was used for refinement of magnification, resolution, envelope correction and atomic B-factors. This was alternated with RSRef-embedded CNS was used for molecular dynamics optimization (1st round) and stereochemically-restrained all-atom least-squares optimization.
Least-squares residual REAL emd_22854_msk_1.map emd_22854_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 -300 -300 -300 600 600 600 306.30002 306.30002 306.30002 90.0 90.0 90.0 Y X Z -0.013762 0.0433061 0.000036581197 0.0039938157 0.5105 0.5105 0.5105 AUTHOR Full particle, unsharpened Relion map, low pass filtered beyond FSC of 1.56 A. See also cropped version. emd_22854_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 286 218 195 -175 -63 114 286 218 195 146.003 111.289 99.5475 90.0 90.0 90.0 X Y Z -0.177197 0.37223 0.00067535345 0.023356553 0.5105 0.5105 0.5105 AUTHOR Relion map, sharpened using volume-whitening routine of cisTEM, and cropped ~20 Angstrom outside deposited subunit coordinates for ease of comparison. emd_22854_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 286 218 195 -175 -63 114 286 218 195 146.003 111.289 99.5475 90.0 90.0 90.0 X Y Z -0.013762 0.0433061 0.00068423955 0.0057823216 0.5105 0.5105 0.5105 AUTHOR Unsharpened Relion map, cropped ~20 Angstrom outside subunit coordinates deposited, for ease of visualization. emd_22854_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 -300 -300 -300 600 600 600 306.30002 306.30002 306.30002 90.0 90.0 90.0 Y X Z -0.0246831 0.0762925 -0.00001122534 0.006213629 0.5105 0.5105 0.5105 AUTHOR Relion half map 1. emd_22854_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 -300 -300 -300 600 600 600 306.30002 306.30002 306.30002 90.0 90.0 90.0 Y X Z -0.0241097 0.0773064 -0.000015477639 0.00621679 0.5105 0.5105 0.5105 AUTHOR Relion half map 2.