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Yorodumi- EMDB-42891: Herpes simplex virus 1 polymerase W781V mutant holoenzyme bound t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42891 | |||||||||
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Title | Herpes simplex virus 1 polymerase W781V mutant holoenzyme bound to DNA in editing conformation | |||||||||
Map data | sharpened map after polishing | |||||||||
Sample |
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Keywords | herpes simplex virus / replication / DNA polymerase holoenzyme / W781V / editing conformation / TRANSFERASE-DNA complex / VIRAL PROTEIN | |||||||||
Function / homology | : / : Function and homology information | |||||||||
Biological species | Human herpesvirus 1 (strain KOS) / Human alphaherpesvirus 1 strain KOS / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.1 Å | |||||||||
Authors | Pan J / Abraham J / Coen DM / Shankar S / Yang P / Hogle J | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Cell / Year: 2024 Title: Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance. Authors: Sundaresh Shankar / Junhua Pan / Pan Yang / Yuemin Bian / Gábor Oroszlán / Zishuo Yu / Purba Mukherjee / David J Filman / James M Hogle / Mrinal Shekhar / Donald M Coen / Jonathan Abraham / Abstract: DNA polymerases are important drug targets, and many structural studies have captured them in distinct conformations. However, a detailed understanding of the impact of polymerase conformational ...DNA polymerases are important drug targets, and many structural studies have captured them in distinct conformations. However, a detailed understanding of the impact of polymerase conformational dynamics on drug resistance is lacking. We determined cryoelectron microscopy (cryo-EM) structures of DNA-bound herpes simplex virus polymerase holoenzyme in multiple conformations and interacting with antivirals in clinical use. These structures reveal how the catalytic subunit Pol and the processivity factor UL42 bind DNA to promote processive DNA synthesis. Unexpectedly, in the absence of an incoming nucleotide, we observed Pol in multiple conformations with the closed state sampled by the fingers domain. Drug-bound structures reveal how antivirals may selectively bind enzymes that more readily adopt the closed conformation. Molecular dynamics simulations and the cryo-EM structure of a drug-resistant mutant indicate that some resistance mutations modulate conformational dynamics rather than directly impacting drug binding, thus clarifying mechanisms that drive drug selectivity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42891.map.gz | 14.6 MB | EMDB map data format | |
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Header (meta data) | emd-42891-v30.xml emd-42891.xml | 30.7 KB 30.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42891_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_42891.png | 38.8 KB | ||
Filedesc metadata | emd-42891.cif.gz | 7.3 KB | ||
Others | emd_42891_additional_1.map.gz emd_42891_additional_2.map.gz emd_42891_additional_3.map.gz emd_42891_half_map_1.map.gz emd_42891_half_map_2.map.gz | 13.9 MB 14 MB 11.8 MB 11.9 MB 11.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42891 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42891 | HTTPS FTP |
-Validation report
Summary document | emd_42891_validation.pdf.gz | 809.1 KB | Display | EMDB validaton report |
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Full document | emd_42891_full_validation.pdf.gz | 808.7 KB | Display | |
Data in XML | emd_42891_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_42891_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42891 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42891 | HTTPS FTP |
-Related structure data
Related structure data | 8exxC 8v1qC 8v1rC 8v1sC 8v1tC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42891.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map after polishing | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.65 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : HSV-1 DNA polymerase W781V mutant holoenzyme in editing complex
Entire | Name: HSV-1 DNA polymerase W781V mutant holoenzyme in editing complex |
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Components |
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-Supramolecule #1: HSV-1 DNA polymerase W781V mutant holoenzyme in editing complex
Supramolecule | Name: HSV-1 DNA polymerase W781V mutant holoenzyme in editing complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Herpes simplex virus type 1 KOS strain polymerase W781V mutant holoenzyme UL30W781V:UL42 in complex with primer DNA that has a 3'-end mismatch with template DNA |
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Source (natural) | Organism: Human herpesvirus 1 (strain KOS) |
Molecular weight | Theoretical: 197 KDa |
-Macromolecule #1: DNA polymerase
Macromolecule | Name: DNA polymerase / type: protein_or_peptide / ID: 1 Details: Herpes simplex virus type 1 (KOS strain) DNA polymerase UL30 with its N-terminal 42 residues deleted and replaced by an N-terminal poly-histidine tag in the expression construct Enantiomer: LEVO |
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Source (natural) | Organism: Human alphaherpesvirus 1 strain KOS / Strain: KOS |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: HHHHHHNFYN PYLAPVGTQQ KPTGPTQRHT YYSECDEFRF IAPRVLDEDA PPEKRAGVHD GHLKRAPKVY CGGDERDVLR VGSGGFWPRR SRLWGGVDHA PAGFNPTVTV FHVYDILENV EHAYGMRAAQ FHARFMDAIT PTGTVITLLG LTPEGHRVAV HVYGTRQYFY ...String: HHHHHHNFYN PYLAPVGTQQ KPTGPTQRHT YYSECDEFRF IAPRVLDEDA PPEKRAGVHD GHLKRAPKVY CGGDERDVLR VGSGGFWPRR SRLWGGVDHA PAGFNPTVTV FHVYDILENV EHAYGMRAAQ FHARFMDAIT PTGTVITLLG LTPEGHRVAV HVYGTRQYFY MNKEEVDRHL QCRAPRDLCE RMAAALRESP GASFRGISAD HFEAEVVERT DVYYYETRPA LFYRVYVRSG RVLSYLCDNF CPAIKKYEGG VDATTRFILD NPGFVTFGWY RLKPGRNNTL AQPRAPMAFG TSSDVEFNCT ADNLAIEGGM SDLPAYKLMC FDIECKAGGE DELAFPVAGH PEDLVIQISC LLYDLSTTAL EHVLLFSLGS CDLPESHLNE LAARGLPTPV VLEFDSEFEM LLAFMTLVKQ YGPEFVTGYN IINFDWPFLL AKLTDIYKVP LDGYGRMNGR GVFRVWDIGQ SHFQKRSKIK VNGMVNIDMY GIITDKIKLS SYKLNAVAEA VLKDKKKDLS YRDIPAYYAT GPAQRGVIGE YCIQDSLLVG QLFFKFLPHL ELSAVARLAG INITRTIYDG QQIRVFTCLL RLADQKGFIL PDTQGRFRGA GGEAPKRPAA AREDEERPEE EGEDEDEREE GGGEREPEGA RETAGRHVGY QGARVLDPTS GFHVNPVVVF DFASLYPSII QAHNLCFSTL SLRADAVAHL EAGKDYLEIE VGGRRLFFVK AHVRESLLSI LLRDVLAMRK QIRSRIPQSS PEEAVLLDKQ QAAIKVVCNS VYGFTGVQHG LLPCLHVAAT VTTIGREMLL ATREYVHARW AAFEQLLADF PEAADMRAPG PYSMRIIYGD TDSIFVLCRG LTAAGLTAMG DKMASHISRA LFLPPIKLEC EKTFTKLLLI AKKKYIGVIY GGKMLIKGVD LVRKNNCAFI NRTSRALVDL LFYDDTVSGA AAALAERPAE EWLARPLPEG LQAFGAVLVD AHRRITDPER DIQDFVLTAE LSRHPRAYTN KRLAHLTVYY KLMARRAQVP SIKDRIPYVI VAQTREVEET VARLAALREL DAAAPGDEPA PPAALPSPAK RPRETPSHAD PPGGASKPRK LLVSELAEDP AYAIAHGVAL NTDYYFSHLL GAACVTFKAL FGNNAKITES LLKRFIPEVW HPPDDVAARL RAAGFGAVGA GATAEETRRM LHRAFDTLA UniProtKB: UNIPROTKB: AFE62858 |
-Macromolecule #2: DNA polymerase processivity factor
Macromolecule | Name: DNA polymerase processivity factor / type: protein_or_peptide / ID: 2 Details: Herpes simplex virus type 1 (KOS strain) processivity factor UL42 residues 1-340 preceding a maltose binding protein (MBP) tag and a PreScission protease cleavage site (MBP-PP-UL42dC340)) Enantiomer: LEVO |
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Source (natural) | Organism: Human alphaherpesvirus 1 strain KOS |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MTDSPGGVAP ASPVEDASDA SLGQPEEGAP CQVVLQGAEL NGILQAFAPL RTSLLDSLLV MGDRGILIHN TIFGEQVFLP LEHSQFSRYR WRGPTAAFLS LVDQKRSLLS VFRANQYPDL RRVELAITGQ APFRTLVQRI WTTTSDGEAV ELASETLMKR ELTSFVVLVP ...String: MTDSPGGVAP ASPVEDASDA SLGQPEEGAP CQVVLQGAEL NGILQAFAPL RTSLLDSLLV MGDRGILIHN TIFGEQVFLP LEHSQFSRYR WRGPTAAFLS LVDQKRSLLS VFRANQYPDL RRVELAITGQ APFRTLVQRI WTTTSDGEAV ELASETLMKR ELTSFVVLVP QGTPDVQLRL TRPQLTKVLN ATGADSATPT TFELGVNGKF SVFTTSTCVT FAAREEGVSS STSTQVQILS NALTKAGQAA ANAKTVYGEN THRTFSVVVD DCSMRAVLRR LQVAGGTLKF FLTTPVPSLC VTATGPNAVS AVFLLKPQKI CLDWLGHSQG SPSAGSSASR UniProtKB: UNIPROTKB: AFE62870 |
-Macromolecule #3: DNA primer
Macromolecule | Name: DNA primer / type: dna / ID: 3 / Details: 3'-deoxy primer DNA strand / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Sequence | String: GATTACGAAT TCGAGCTCGG TACCCGGGGA T(DOC) |
-Macromolecule #4: DNA template
Macromolecule | Name: DNA template / type: dna / ID: 4 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Sequence | String: CACACACACA CACACACAGA TCCCCGGGTA CCGAGCTCGA ATTCGTAATC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.38 mg/mL |
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Buffer | pH: 7.5 Details: 25 mM HEPES, pH 7.5, 150 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine (TCEP) |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa Details: Pelco easiGlow at 15 mA for 30 seconds under 0.39 mBar (i.e. 39 Pa) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: 3 microliters of sample were blotted for 3 seconds with filter paper saturated under 100% humidity prior to plunging.. |
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 77.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 1678 / Average exposure time: 1.5 sec. / Average electron dose: 58.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 60606 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |