2024-10-16 REL RCSB RCSB RCSB 2022-10-26 2024-09-04 2024-09-04 2024-10-16 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R21 AI141940 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01 AI019838 United States Herpes simplex virus 1 polymerase holoenzyme bound to DNA and foscarnet (pre-translocation state) Pan J Abraham J Coen DM Shankar S Yang P Hogle J herpes simplex virus, replication, DNA polymerase holoenzyme, UL30, UL42, pre-translocation, foscarnet, VIRAL PROTEIN, VIRAL PROTEIN-DNA complex Shankar S Pan J Yang P Bian Y Oroszlan G Yu Z Mukherjee P Filman DJ Hogle JM Shekhar M Coen DM Abraham J Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance. Cell 187 5572 5586.e15 2024 39197451 doi:10.1016/j.cell.2024.07.048 1097-4172 EMD-28664 other EM volume
Herpes simplex virus 1 DNA polymerase holoenzyme bound to DNA template and primer, dNTP-free (editing mode)
 EMD-42888 other EM volume
Herpes simplex virus 1 polymerase holoenzyme bound to DNA and DTTP in closed conformation
 EMD-42891 other EM volume
Herpes simplex virus 1 polymerase W781V mutant holoenzyme bound to DNA in editing conformation
 EMD-42889 other EM volume
Herpes simplex virus 1 polymerase holoenzyme bound to mismatched DNA in editing conformation
 EMD-42890 other EM volume
Herpes simplex virus 1 polymerase holoenzyme bound to DNA and acyclovir triphosphate in closed conformation
 EMD-42887 other EM volume
Herpes simplex virus 1 polymerase holoenzyme bound to DNA in both open/closed conformations
 8exx FULLOVERLAP Herpes simplex virus 1 polymerase holoenzyme UL30:UL42 in complex with DNA and foscarnet Herpes simplex virus 1 polymerase holoenzyme UL30:UL42 in complex with DNA and foscarnet 0 2 3 4
each complex consists of one HSV-1 UL30, one HSV-1 UL42, one template DNA, one primer DNA (3'-deoxyl), and one foscarnet molecule.
Human herpesvirus 1 (strain KOS) KOS 0.197 DNA polymerase Human alphaherpesvirus 1 strain KOS 0.133614344
Herpes simplex virus type 1 (KOS strain) DNA polymerase catalytic subunit UL30 with its N-terminal 42 residues deleted and replaced by an N-terminal poly-histidine tag in the expression construct.
1 Spodoptera frugiperda LEVO HHHHHHNFYNPYLAPVGTQQKPTGPTQRHTYYSECDEFRFIAPRVLDEDAPPEKRAGVHDGHLKRAPKVYCGGDERDVLR VGSGGFWPRRSRLWGGVDHAPAGFNPTVTVFHVYDILENVEHAYGMRAAQFHARFMDAITPTGTVITLLGLTPEGHRVAV HVYGTRQYFYMNKEEVDRHLQCRAPRDLCERMAAALRESPGASFRGISADHFEAEVVERTDVYYYETRPALFYRVYVRSG RVLSYLCDNFCPAIKKYEGGVDATTRFILDNPGFVTFGWYRLKPGRNNTLAQPRAPMAFGTSSDVEFNCTADNLAIEGGM SDLPAYKLMCFDIECKAGGEDELAFPVAGHPEDLVIQISCLLYDLSTTALEHVLLFSLGSCDLPESHLNELAARGLPTPV VLEFDSEFEMLLAFMTLVKQYGPEFVTGYNIINFDWPFLLAKLTDIYKVPLDGYGRMNGRGVFRVWDIGQSHFQKRSKIK VNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLKDKKKDLSYRDIPAYYATGPAQRGVIGEYCIQDSLLVGQLFFKFLPHL ELSAVARLAGINITRTIYDGQQIRVFTCLLRLADQKGFILPDTQGRFRGAGGEAPKRPAAAREDEERPEEEGEDEDEREE GGGEREPEGARETAGRHVGYQGARVLDPTSGFHVNPVVVFDFASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKDYLEIE VGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLLDKQQAAIKVVCNSVYGFTGVQHGLLPCLHVAAT VTTIGREMLLATREYVHARWAAFEQLLADFPEAADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAMGDKMASHISRA LFLPPIKLECEKTFTKLLLIAKKKYIGVIYGGKMLIKGVDLVRKNNCAFINRTSRALVDLLFYDDTVSGAAAALAERPAE EWLARPLPEGLQAFGAVLVDAHRRITDPERDIQDFVLTAELSRHPRAYTNKRLAHLTVYYKLMARRAQVPSIKDRIPYVI VAQTREVEETVARLAALRELDAAAPGDEPAPPAALPSPAKRPRETPSHADPPGGASKPRKLLVSELAEDPAYAIAHGVAL NTDYYFSHLLGAACVTFKALFGNNAKITESLLKRFIPEVWHPPDDVAARLRAAGFGAVGAGATAEETRRMLHRAFDTLA H9E937 2.7.7.7 DNA polymerase processivity factor Human alphaherpesvirus 1 strain KOS 0.03634618
Herpes simplex virus type 1 (KOS strain) DNA polymerase processivity factor UL42 residues 1-340 tagged with a PreScission protease cleavage site followed by a maltose binding protein (MBP) tag in the expression construct
1 Escherichia coli BL21(DE3) LEVO MTDSPGGVAPASPVEDASDASLGQPEEGAPCQVVLQGAELNGILQAFAPLRTSLLDSLLVMGDRGILIHNTIFGEQVFLP LEHSQFSRYRWRGPTAAFLSLVDQKRSLLSVFRANQYPDLRRVELAITGQAPFRTLVQRIWTTTSDGEAVELASETLMKR ELTSFVVLVPQGTPDVQLRLTRPQLTKVLNATGADSATPTTFELGVNGKFSVFTTSTCVTFAAREEGVSSSTSTQVQILS NALTKAGQAAANAKTVYGENTHRTFSVVVDDCSMRAVLRRLQVAGGTLKFFLTTPVPSLCVTATGPNAVSAVFLLKPQKI CLDWLGHSQGSPSAGSSASR H9E949 Primer DNA (32-MER) synthetic construct 0.009866352999999998
3'-deoxyl primer DNA strand, no mismatch with template strand
1 (DG)(DA)(DT)(DT)(DA)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DA)(DG)(DC)(DT)(DC)(DG)(DG) (DT)(DA)(DC)(DC)(DC)(DG)(DG)(DG)(DG)(DA)(DT)(DOC) DNA Template DNA (50-MER) synthetic construct 0.015223799
no mismatch with primer strand
1 (DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DG)(DA) (DT)(DC)(DC)(DC)(DC)(DG)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DA)(DG)(DC)(DT)(DC)(DG)(DA) (DA)(DT)(DT)(DC)(DG)(DT)(DA)(DA)(DT)(DC) DNA MAGNESIUM ION 2.4305e-05 3 MG PHOSPHONOFORMIC ACID 0.000126005 1 PPF singleParticle particle 1.3 7.5
25 mM HEPES, pH 7.5, 150 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine (TCEP)
 Quantifoil R1.2/1.3 COPPER 400 GLOW DISCHARGE AIR 0.039
grids were discharge in a Pelco easiGlow at 15 mA for 30 seconds under 0.39 mBar
 ETHANE 100 298 FEI VITROBOT MARK IV
3 microliters of sample were blotted for 3 seconds with filter paper saturated under 100% humidity prior to plunging..
This sample was monodisperse.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 1.0 2.5 2.5 105000.0 60606.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 77.0 GIF Bioquantum 20 GATAN K3 (6k x 4k) 5760 4092 1 4914 1.5 53.11 1 2090711
ab initio using Relion
 5 C1 FOURIER SPACE 3.3 FSC 0.143 CUT-OFF RELION 3.1 264472 RANDOM ASSIGNMENT RELION 3.0.8 MAXIMUM LIKELIHOOD RELION 3.1 5 84464.0 RELION 3.1 emd_28663.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 Z Y X -27.213373000000001 46.251519999999999 0.000000000002639 1.0 0.825 0.825 0.825 4.0 AUTHOR HSV-1 polymerase holoenzyme bound by DNA and foscarnet (pre-translocation state) sharpened map OTHER
rigid body, minimization_global, local_grid_search, adp refinement
correlation coefficient REAL 67.950000000000003 emd_28663_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.013890602 0.039899457 0.0000026079322 0.001162774 0.825 0.825 0.825 AUTHOR unfiltered, unsharpened map emd_28663_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.022919416 0.044987503 0.0000028482405 0.0018920301 0.825 0.825 0.825 AUTHOR half map 1 emd_28663_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 264.0 264.0 264.0 90.0 90.0 90.0 X Y Z -0.024938155 0.04561242 0.0000023973644 0.0018765422 0.825 0.825 0.825 AUTHOR half map 2