2024-10-16 REL RCSB RCSB RCSB 2019-02-12 2019-04-03 2019-06-12 2024-10-16 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM122564 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM066875 United States Cryo-EM structure of AAV-2 in complex with AAVR PKD domains 1 and 2 Meyer NL Xie Q AAV, AAVR, receptor, coreceptor, VIRUS, KIAA0319L, PKD, parvovirus Meyer NL Hu G Davulcu O Xie Q Noble AJ Yoshioka C Gingerich DS Trzynka A David L Stagg SM Chapman MS Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR. Elife US 8 2019 31115336 doi:10.7554/eLife.44707 2050-084X EMD-0621 other EM volume
Cryo-Electron Tomography of AAV-2 complexed with MBP fusion construct of AAVR PKD domains 1-5, class 1
 EMD-0622 other EM volume
Cryo-Electron Tomography of AAV-2 complexed with MBP fusion construct of AAVR PKD domains 1-5, class 2
 EMD-0623 other EM volume
Cryo-Electron Tomography of AAV-2 complexed with MBP fusion construct of AAVR PKD domains 1-5, class 3
 EMD-0624 other EM volume
Cryo-Electron Tomography of AAV-2 complexed with MBP fusion construct of AAVR PKD domains 1-5, class 4
 6nz0 FULLOVERLAP Adeno-associated virus - 2 Adeno-associated virus - 2 0 1 2
AAV-2 virus-like particles expressed in Sf9 cells using Invitrogen's Bac-to-Bac expression system
Adeno-associated virus - 2 Homo sapiens 0.022 250.0 1 VIRUS-LIKE PARTICLE SEROTYPE false true Binary complex of AAV-2 with a fragment of its cellular receptor, AAVR or dyslexia-associated protein KIAA0319-like protein. 1 1
Expressed N-terminally His6-tagged fragment of AAVR containing the PKD1 and PKD2 domains.
Homo sapiens Dyslexia-associated protein KIAA0319-like protein Homo sapiens 0.031837384999999996 1 Escherichia coli LEVO MASVSAGESVQITLPKNEVQLNAYVLQEPPKGETYTYDWQLITHPRDYSGEMEGKHSQILKLSKLTPGLYEFKVIVEGQN AHGEGYVNVTVKPEPRKNRPPIAIVSPQFQEISLPTTSTVIDGSQSTDDDKIVQYHWEELKGPLREEKISEDTAILKLSK LVPGNYTFSLTVVDSDGATNSTTANLTVNKAVDYPPVANAGPNQVITLPQNSITLFGNQSTDDHGITSYEWSLSPSSKGK VVEMQGVRTPTLQLSAMQEGDYTYQLTVTDTIGQQATAQVTVIVQPENNK Q8IZA0 Capsid protein VP1 Adeno-associated virus - 2 0.082077445 1 Spodoptera frugiperda LEVO MAADGYLPDWLEDTLSEGIRQWWKLKPGPPPPKPAERHKDDSRGLVLPGYKYLGPFNGLDKGEPVNEADAAALEHDKAYD RQLDSGDNPYLKYNHADAEFQERLKEDTSFGGNLGRAVFQAKKRVLEPLGLVEEPVKTAPGKKRPVEHSPVEPDSSSGTG KAGQQPARKRLNFGQTGDADSVPDPQPLGQPPAAPSGLGTNTMATGSGAPMADNNEGADGVGNSSGNWHCDSTWMGDRVI TTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQV KEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMVPQYGYLTLNNGSQAVCRSSFYCLEYFPS QMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPG PCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVLIFGKQGSEKTNVDIEKVMIT DEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGVLPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLK HPPPQILIKNTPVPANPSTTFSAAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVY SEPRPIGTRYLTRNL P03135 MAGNESIUM ION 2.4305e-05 1 MG water 1.8015e-05 143 HOH singleParticle particle 0.1 7.4 25.0 HEPES 150.0 NaCl 50.0 MgCl2 COPPER 400 CARBON LACEY GLOW DISCHARGE AIR 0.039
Glow discharge settings: Pelco easiGlow, 25s, 25mA, 0.39mBar, negative polarity Grid: Ted Pella Cat#01824, ultrathin carbon film (<3nm) on lacey carbon support film
 ETHANE 100 298.15 FEI VITROBOT MARK IV
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)..
Virus-like particles at 0.10 mg/mL were adhered to thin continuous carbon-coated grids, then, after initial blotting, AAVR-PKD1-2 was added at 0.74 mg/mL (a 10-fold molar excess over AAV2 subunits) before blotting again.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 -0.8 -2.0 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) SUPER-RESOLUTION 7676 7420 1 2329 40.0 25.4 1 34450
RELION Autopicker using 3D AAV-2 reference filtered to 20A with 15 degree sampling
 1 I 2.4 FSC 0.143 CUT-OFF RELION 3.0b 21373 MAXIMUM LIKELIHOOD RELION 3.0b MAXIMUM LIKELIHOOD RELION 3.0b 2 RELION 3.0b emd_0553.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 -192 -192 -192 384 384 384 401.664 401.664 401.664 90.0 90.0 90.0 X Y Z -0.30914757 0.5151396 0.0015742391 0.02952454 1.046 1.046 1.046 0.053 AUTHOR EM sharpened map 1LP3 A 217-735 PDB experimental model FLEXIBLE FIT
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.
Map values at grid points within 2 Angstrom of atoms REAL emd_0553_msk_1.map emd_0553_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 -192 -192 -192 384 384 384 401.664 401.664 401.664 90.0 90.0 90.0 X Y Z -0.018904606 0.052232154 0.0005937355 0.0042323144 1.046 1.046 1.046 AUTHOR half map 2 emd_0553_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 -192 -192 -192 384 384 384 401.664 401.664 401.664 90.0 90.0 90.0 X Y Z -0.01887643 0.050408244 0.00058610196 0.004221608 1.046 1.046 1.046 AUTHOR half map 1