2025-04-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2024-09-20 2025-03-26 2025-03-26 2025-04-09 Spanish Ministry of Science, Innovation, and Universities PID2021-126130OB-I00 Spain Academy of Finland grant #314939 Finland Research Council of Norway project ID #2520855 Norway Wellcome Trust eBIC access proposal CM30316 United Kingdom Spanish Ministry of Science, Innovation, and Universities access RES BCV-2022-3-0015 Spain Spanish Ministry of Science, Innovation, and Universities CEX2021-001136-S Spain Giant Jyvaskylavirus at 6.3 Ang resolution Abrescia NG Arriaga I de Freitas Almeida GM Sundberg LR Ravantti J Giant virus, cryo-EM, genomic, NCLDV, Marseilleviridae family, VIRUS Almeida GMF Arriaga I de Azevedo BL Leppanen M Abrahao JS Andreani J Zabeo D Ravantti JJ Abrescia NGA Sundberg LR Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland. Elife US 13 2025 40131223 doi:10.7554/eLife.103492 2050-084X Jyvaskylavirus Jyvaskylavirus 0 1
Full virion
Jyvaskylavirus Acanthamoeba castellanii Jyvaskylavirus ORF184 2500.0 309 VIRION OTHER false false Jyvaskylavirus Acanthamoeba castellanii XXXXX other singleParticle particle 7.4 120.0 NaCl sodium chloride 4.0 MgSO4 magnesium sulfate 4.0 CaCl2 calcium chloride 142.0 Na2HPO4 disodium phosphate 136.0 KH2PO4 monopotassium phosphate Quantifoil R2/1 COPPER 300 CARBON HOLEY CARBON CONTINUOUS GLOW DISCHARGE AIR 0.0002
8-9 mA
 ETHANE 95 277.15 FEI VITROBOT MARK IV
Also Automatic Plunge Freezer EM2 (Leica) was used (see publication)..
TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.6 3.0 64000.0 GATAN K3 BIOQUANTUM (6k x 4k) 45.0 1
ab initio
 I 6.3 FSC 0.143 CUT-OFF RELION 3742 PROJECTION MATCHING RELION PROJECTION MATCHING emd_51613.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 2304 2304 2304 0 0 0 2304 2304 2304 3087.36 3087.36 3087.36 90.0 90.0 90.0 X Y Z -0.00902783 0.020209888 0.0015317714 0.0023726863 1.34 1.34 1.34 0.005 AUTHOR IMPORTANT: Map has been binned from the original boxel size (1.34 A/px). Post-processed map, no masked, using the automatic B-factor sharpening by RELION. AlphaFold in silico model Other integrative model
ModelAngelo
 Other integrative model
Please see publication
 RIGID BODY FIT
Please keep in mind that the predicted Jyvaskylavirus PDB models using ModelAngelo and Alphafold have been deposited at the Biostudies website (https://www.ebi.ac.uk/biostudies/). Please refer to the published article for the corresponding entry code.
 emd_51613_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 2304 2304 2304 0 0 0 2304 2304 2304 3087.36 3087.36 3087.36 90.0 90.0 90.0 X Y Z -0.00701596 0.017929427 0.0015247458 0.0022041001 1.34 1.34 1.34 AUTHOR IMPORTANT: Map has been binned from the original boxel size (1.34 A/px). Unfiltered, unmasked, half map 2 from the 3D auto refinement by RELION emd_51613_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 2304 2304 2304 0 0 0 2304 2304 2304 3087.36 3087.36 3087.36 90.0 90.0 90.0 X Y Z -0.008503503 0.020297617 0.0015387957 0.0022346913 1.34 1.34 1.34 AUTHOR IMPORTANT: Map has been binned from the original boxel size (1.34 A/px). Unfiltered, unmasked, half map 1 from the 3D auto refinement by RELION