2025-12-17 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATA_COLLECTION em_software _em_software.details _em_software.name _em_software.version OTHER atom_sites cell _atom_sites.fract_transf_matrix[1][1] _atom_sites.fract_transf_matrix[2][2] _atom_sites.fract_transf_matrix[3][3] _cell.length_a _cell.length_b _cell.length_c OTHER cell _cell.Z_PDB OTHER symmetry _symmetry.Int_Tables_number _symmetry.space_group_name_H-M REFINEMENT_DESCRIPTION chem_comp_atom chem_comp_bond database_2 pdbx_struct_oper_list refine _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.type _refine.ls_d_res_high _refine.ls_d_res_low STRUCTURE_SUMMARY atom_site chem_comp chem_comp_atom chem_comp_bond em_admin pdbx_entity_nonpoly pdbx_entry_details pdbx_nonpoly_scheme pdbx_unobs_or_zero_occ_atoms struct_site _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.type_symbol _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.type _chem_comp_atom.atom_id _chem_comp_atom.comp_id _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.type_symbol _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _em_admin.last_update _pdbx_entity_nonpoly.comp_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _struct_site.details _struct_site.pdbx_auth_comp_id PDBe PDBe 2016-06-08 2016-08-31 2017-03-29 2025-12-17 European Research Council 355855 Structure of deformed wing virus, a honeybee pathogen Skubnik K Novacek J Deformed wing virus, Picornavirales, Iflaviridae, Iflavirus, viral protein Skubnik K Novacek J Fuzik T Pridal A Paxton RJ Plevka P Structure of deformed wing virus, a major honey bee pathogen. Proc. Natl. Acad. Sci. U.S.A. US 114 3210 3215 2017 28270616 doi:10.1073/pnas.1615695114 1091-6490 0040 PNASA6 5l8q FULLOVERLAP EMDB EMD-4014 associated EM volume Deformed wing virus Deformed wing virus 0 1 2 3 4
Virus was purified from honeybee pupae
Deformed wing virus Apis mellifera 390.0 3 VIRION OTHER false false VP1 Deformed wing virus 0.028679272999999998 1 LEVO GEESRNTTVLDTTTTLQSSGFGRAFFGEAFNDLKTLMRRYQLYGQLLLSVTTDKDIDHCMFTFPCLPQGLALDIGSAGSP HEIFNRCRDGIIPLIASGYRFYRGDLRYKIVFPSNVNSNIWVQHRPDRRLEGWSAAKIVNCDAVSTGQGVYNHGYASHIQ ITRVNNVIELEVPFYNATCYNYLQAFNASSAASSYAVSLGEISVGFQATSDDIASIVNKPVTIYYSIGDGMQFSQWVGYQ PMMILDQLPAPVVRAVPE L0CTV4 VP2 Deformed wing virus 0.0283609 1 LEVO MDNPNPGPDGEGEVELEKDSNVVLTTQRDPSTSIPAPVSVKWSRWTSNDVVDDYATITSRWYQIAEFVWSKDDPFDKELA RLILPRALLSSIEANSDAICDVPNTIPFKVHAYWRGDMEVRVQINSNKFQVGQLQATWYYSDHENLNISSKRSVYGFSQM DHALISASASNEAKLVIPFKHVYPFLPTRIVPDWTTGILDMGALNIRVIAPLRMSATGPTTCNVVVFIKLNNSEFTGTSS GKFYASQIRAKPE E0YTW0 VP3 Deformed wing virus 0.046697582 1 LEVO DNPSYQQSPRHFVPTGMHSLALGTNLVEPLHALRLDAAGTTQHPVGCAPDEDMTVSSIASRYGLIRRVQWKKDHAKGSLL LQLDADPFVEQRIEGTNPISLYWFAPVGVVSSMFMQWRGSLEYRFDIIASQFHTGRLIVGYVPGLTASLQLQMDYMKLKS SSYVVFDLQESNSFTFEVPYVSYRPWWVRKYGGNYLPSSTDAPSTLFMYVQVPLIPMEAVSDTIDINVYVRGGSSFEVCV PVQPSLGLNWNTDFILRNDEEYRAKTGYAPYYAGVWHSFNNSNSLVFRWGSASDQIAQWPTISVPRGELAFLRIKDGKQA AVGTQPWRTMVVWPSGHGYNIGIPTYNAERARQLAQHLYGGGSLTDEKAKQLFVPANQQGPGKVSNGNPVWEVMRAPLAT QRAHIQDFEFIEAIPE Q7TG18 URIDINE-5'-MONOPHOSPHATE Apis mellifera 0.000324181 1 U5P singleParticle particle 2.5 7.4
Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich
 Quantifoil R2/1 COPPER 300 GLOW DISCHARGE NITROGEN 0.007 ETHANE 100 298 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.0 4.0 75000.0 74235.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON II (4k x 4k) COUNTING 4096 4096 2-7 1 26 1.0 15.0 1 141860 CTFFIND 4 PHASE FLIPPING AND AMPLITUDE CORRECTION
Model obtained by crystallography with resolution 7.5
 1 I FOURIER SPACE 3.5 FSC 0.143 CUT-OFF RELION 1.4 relion_refine_mpi 26540 OTHER PROJECTION MATCHING RELION 1.4 relion_refine_mpi
Relion 3D auto refinement
 5 12000.0 RELION 1.4 relion_refine_mpi
Relion 3D classfication - reclassification after initial 3D refinement
 emd_4014.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 -256 -256 -256 512 512 512 542.208 542.208 542.208 90.0 90.0 90.0 X Y Z -0.6789989 0.9588455 0.0022389216 0.040165383 1.059 1.059 1.059 0.09 AUTHOR OTHER R-factor REAL