2023-08-16 REL PDBe PDBe PDBe 2022-08-10 2022-11-09 2022-11-09 2023-08-16 Agence Nationale de la Recherche (ANR) ANR-13-BSV8-0014 France Agence Nationale de la Recherche (ANR) ANR-15-IDEX-02 France Agence Nationale de la Recherche (ANR) ANR-10-INBS-0005-02 France Agence Nationale de la Recherche (ANR) ANR-17-EURE-0003 France Agence Nationale de la Recherche (ANR) PoxRep France Vaccinia virus DNA helicase D5 residues 323-785 hexamer with bound DNA processed in C1 Burmeister WP Hutin S Ling WL Grimm C Schoehn G DNA helicase, D5_N domain, DUF5906 domain, Pox_D5 domain, SF3 helicase, VIRAL PROTEIN Hutin S Ling WL Tarbouriech N Schoehn G Grimm C Fischer U Burmeister WP The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction. Viruses CH 14 2022 36298761 doi:10.3390/v14102206 1999-4915 8apm FULLOVERLAP Primase D5 C-terminal fragment res. 323 - res. 785 Primase D5 C-terminal fragment res. 323 - res. 785 0 1 2 3
construct
0.325 Primase-helicase D5 fragment residues 323-785 1 1
Obtained after TEV (tobacco etch virus) cleavage of a construct
Vaccinia virus Copenhagen DNA (5'-D(P*CP*CP*GP*AP*AP*TP*CP*A)-3') 1 2 Synthetic construct DNA (5'-D(P*TP*GP*AP*TP*TP*CP*GP*G)-3') 1 3 Synthetic construct Primase D5 Vaccinia virus Copenhagen Copenhagen 0.053495285000000004
obtained after tobacco etch virus protease cleavage with 2 additional N-terminal residues from the cleavage site.
6 Spodoptera frugiperda LEVO AMGNKLFNIAQRILDTNSVLLTERGDYIVWINNSWKFNSEEPLITKLILSIRHQLPKEYSSELLCPRKRKTVEANIRDML VDSVETDTYPDKLPFKNGVLDLVDGMFYSGDDAKKYTCTVSTGFKFDDTKFVEDSPEMEELMNIINDIQPLTDENKKNRE LYEKTLSSCLCGATKGCLTFFFGETATGKSTTKRLLKSAIGDLFVETGQTILTDVLDKGPNPFIANMHLKRSVFCSELPD FACSGSKKIRSDNIKKLTEPCVIGRPCFSNKINNRNHATIIIDTNYKPVFDRIDNALMRRIAVVRFRTHFSQPSGREAAE NNDAYDKVKLLDEGLDGKIQNNRYRFAFLYLLVKWYKKYHVPIMKLYPTPEEIPDFAFYLKIGTLLVSSSVKHIPLMTDL SKKGYILYDNVVTLPLTTFQQKISKYFNSRLFGHDIESFINRHKKFANVSDEYLQYIFIEDISSP P21010 3.6.4.- DNA (5'-D(P*CP*CP*GP*AP*AP*TP*CP*A)-3') synthetic construct 0.009265994
synthetic, at the current resolution the sequence does not matter, the DNA oligomer was end-labelled: biotin-ccgaatcaggaagataacagcggtttagcc3-digoxigenin
1 (DC)(DC)(DG)(DA)(DA)(DT)(DC)(DA)(DG)(DG)(DA)(DA)(DG)(DA)(DT)(DA)(DA)(DC)(DA)(DG) (DC)(DG)(DG)(DT)(DT)(DT)(DA)(DG)(DC)(DC) DNA DNA (5'-D(P*TP*GP*AP*TP*TP*CP*GP*G)-3') synthetic construct 0.00921191
At the current resolution, the base mismatch does not have any impact as it is located in an unpaired part of the DNA.
1 (DG)(DG)(DC)(DT)(DT)(DA)(DG)(DT)(DC)(DC)(DT)(DT)(DC)(DT)(DA)(DT)(DT)(DG)(DT)(DC) (DG)(DC)(DA)(DG)(DA)(DT)(DT)(DC)(DG)(DG) DNA singleParticle particle 0.24 7.0 50.0 C4H12NO3Cl Tris-HCl 50.0 NaCl sodium chloride 100.0 KCl potassium chloride 2.0 MgCl2 magnesium chloride 0.5 C3H8O3 glycerol 10.0 HOCH2CH2SH beta-mercaptoethanol Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY ETHANE 100 293 FEI VITROBOT MARK IV
The sample contained also a dsDNA oligomer in slight stoechiometric excess over hexamers.
 FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.5 1.5 3.0 3.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 1-40 1 830 1.0 1 202659
Using 2D templates
 1 C1 6.6 FSC 0.143 CUT-OFF RELION 3.1 26710 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3 25000.0 RELION 3.1 emd_15575.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 309.76 309.76 309.76 90.0 90.0 90.0 X Y Z -0.028547706 0.07065984 0.00023617754 0.0023804225 1.21 1.21 1.21 0.005 AUTHOR Masked map in C1 from Relion PostProcess OTHER REAL 152.0 emd_15575_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 309.76 309.76 309.76 90.0 90.0 90.0 X Y Z -0.02580253 0.052671935 0.00002446474 0.0030091864 1.21 1.21 1.21 AUTHOR Half map from Relion Refine3D in C1 emd_15575_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 309.76 309.76 309.76 90.0 90.0 90.0 X Y Z -0.023724327 0.05337748 0.000026727612 0.0029998322 1.21 1.21 1.21 AUTHOR Half map from Relion Refine3D in C1