2022-04-13 REL PDBj PDBj PDBj 2021-09-13 2022-02-23 2022-02-23 2022-04-13 Japan Agency for Medical Research and Development (AMED) JP18am0101076 Japan Japan Society for the Promotion of Science (JSPS) JP17K07318 Japan Japan Society for the Promotion of Science (JSPS) 21K06039 Japan Cryo-EM structure of Vaccinia virus scaffolding protein D13 tubular assembly Hyun J Matsunami H Kim TG Wolf M Hyun J Matsunami H Kim TG Wolf M Assembly mechanism of the pleomorphic immature poxvirus scaffold. Nat Commun UK 13 1704 1704 2022 35361762 doi:10.1038/s41467-022-29305-5 2041-1723 EMD-31953 associated EM volume Vaccinia virus scaffolding protein D13 with N-terminal 17 residue truncation, in its tubular assembly Vaccinia virus scaffolding protein D13 with N-terminal 17 residue truncation, in its tubular assembly 0 1
Recombinant D13 was expressed with N-terminal polyhistidine-tag (His-tag) using bacterial expression system. The protein was purified using metal affinity chromatography. His-tag was removed by proteolysis and the protein was further purified using size exclusion chromatography. The final purified protein was trimeric. The protein was assembled into tubes in low salt buffer.
Vaccinia virus WR Escherichia coli BL21(DE3) 54 Vaccinia virus scaffolding protein D13 with N-terminal 17 residue truncation, in its tubular assembly Vaccinia virus WR Escherichia coli BL21(DE3) LEVO RSNVFAVDSQIPTLYMPQYISLSGVMTNDGPDNQAIASFEIRDQYITALNHLVLSLELPEVK GMGRFGYVPYVGYKCINHVSISSCNGVIWEIEGEELYNNCINNTIALKHSGYSSELNDISIGLTPNDTIKEPSTVYVYIK TPFDVEDTFSSLKLSDSKITVTVTFNPVSDIVIRDSSFDFETFNKEFVYVPELSFIGYMVKNVQIKPSFIEKPRRVIGQI NQPTATVTEVHAATSLSVYTKPYYGNTDNKFISYPGYSQDEKDYIDAYVSRLLDDLVIVSDGPPTGYPESAEIVEVPEDG IVSIQDADVYVKIDNVPDNMSVYLHTNLLMFGTRKNSFIYNISKKFSAITGTYSDATKRTIFAHISHSINIIDTSIPVSL WTSQRNVYNGDNRSAESKAKDLFINDPFIKGIDFKNKTDIISRLEVRFGNDVLYSENGPISRIYNELLTKSNNGTRTLTF NFTPKIFFRPTTITANVSRGKDKLSVRVVYSTMDVNHPIYYVQKQLVVVCNDLYKVSYDQGVSITKIMG helical particle 0.12 8.0 50.0 NH2C(CH2OH)3HCl Tris hydrochloride 150.0 NaCl Sodium chlroride 2.0 HSCH2CH2OH 2-mercapthoethanol Quantifoil R2/2 COPPER 300 CARBON HOLEY PLASMA CLEANING ETHANE-PROPANE 90 277 FEI VITROBOT MARK IV
3 microliter sample volume was loaded onto a holey grid with additional graphene oxide film. 10 sec waiting time, 5 sec blotting time and blot force 0, no delay time were applied before plunging..
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.5 2.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 QUANTUM (4k x 4k) COUNTING 4096 4096 5.0 2 7621 10.0 50.0 1 4 33.86 76.98 C1 FOURIER SPACE 7.33 FSC 0.143 CUT-OFF RELION 3.1 75070 CTFFIND 4.1.9 CTF determination RELION 3.1 CTF correction and refinement 194960 RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 emd_31953.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 1433.6 1433.6 1433.6 90.0 90.0 90.0 X Y Z -9.024279 14.637431 6.845562e-10 0.99999994 2.8 2.8 2.8 4.0 AUTHOR Cryo-EM helical reconstruction of Vaccinia virus scaffold protein D13 tubular assembly. The map has been sharpened using Relion post-processing. The map has been density-normalized (mean=0, s.d=1). 6BEI RIGID BODY FIT REAL emd_31953_msk_1.map emd_31953_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 1433.6 1433.6 1433.6 90.0 90.0 90.0 X Y Z -0.016600206 0.060210597 0.00031925584 0.0067231753 2.8 2.8 2.8 AUTHOR Cryo-EM helical reconstruction of Vaccinia virus scaffold protein D13 tubular assembly (half map 1). emd_31953_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 1433.6 1433.6 1433.6 90.0 90.0 90.0 X Y Z -0.016164042 0.05832962 0.00031677188 0.006668546 2.8 2.8 2.8 AUTHOR Cryo-EM helical reconstruction of Vaccinia virus scaffold protein D13 tubular assembly (half map 2).