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Yorodumi- EMDB-19840: HSV-1 DNA polymerase-processivity factor complex in exonuclease s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19840 | |||||||||
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Title | HSV-1 DNA polymerase-processivity factor complex in exonuclease state with 1-bp DNA mismatch catalytic core focused map | |||||||||
Map data | Focused refinement map in cryoSPARC | |||||||||
Sample |
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Keywords | DNA / Polymerase / Complex / TRANSFERASE | |||||||||
Biological species | Human alphaherpesvirus 1 strain KOS / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||
Authors | Gustavsson E / Grunewald K / Elias P / Hallberg BM | |||||||||
Funding support | Sweden, Germany, 2 items
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Citation | Journal: Nucleic Acids Res / Year: 2024 Title: Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM. Authors: Emil Gustavsson / Kay Grünewald / Per Elias / B Martin Hällberg / Abstract: Herpes simplex virus 1 (HSV-1), a double-stranded DNA virus, replicates using seven essential proteins encoded by its genome. Among these, the UL30 DNA polymerase, complexed with the UL42 ...Herpes simplex virus 1 (HSV-1), a double-stranded DNA virus, replicates using seven essential proteins encoded by its genome. Among these, the UL30 DNA polymerase, complexed with the UL42 processivity factor, orchestrates leading and lagging strand replication of the 152 kb viral genome. UL30 polymerase is a prime target for antiviral therapy, and resistance to current drugs can arise in immunocompromised individuals. Using electron cryo-microscopy (cryo-EM), we unveil the dynamic changes of the UL30/UL42 complex with DNA in three distinct states. First, a pre-translocation state with an open fingers domain ready for nucleotide incorporation. Second, a halted elongation state where the fingers close, trapping dATP in the dNTP pocket. Third, a DNA-editing state involving significant conformational changes to allow DNA realignment for exonuclease activity. Additionally, the flexible UL30 C-terminal domain interacts with UL42, forming an extended positively charged surface binding to DNA, thereby enhancing processive synthesis. These findings highlight substantial structural shifts in the polymerase and its DNA interactions during replication, offering insights for future antiviral drug development. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19840.map.gz | 212.5 MB | EMDB map data format | |
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Header (meta data) | emd-19840-v30.xml emd-19840.xml | 22 KB 22 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19840_fsc.xml | 15.7 KB | Display | FSC data file |
Images | emd_19840.png | 60.3 KB | ||
Masks | emd_19840_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-19840.cif.gz | 6.3 KB | ||
Others | emd_19840_additional_1.map.gz emd_19840_half_map_1.map.gz emd_19840_half_map_2.map.gz | 1.9 MB 391.9 MB 391.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19840 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19840 | HTTPS FTP |
-Validation report
Summary document | emd_19840_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_19840_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_19840_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | emd_19840_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19840 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19840 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19840.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Focused refinement map in cryoSPARC | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19840_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Locally filtered local refinement map from cryoSPARC
File | emd_19840_additional_1.map | ||||||||||||
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Annotation | Locally filtered local refinement map from cryoSPARC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Halfmap A for focused refinement in cryoSPARC
File | emd_19840_half_map_1.map | ||||||||||||
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Annotation | Halfmap A for focused refinement in cryoSPARC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Halfmap B for focused refinement in cryoSPARC
File | emd_19840_half_map_2.map | ||||||||||||
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Annotation | Halfmap B for focused refinement in cryoSPARC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HSV-1 DNA polymerase-processivity factor complex in exonuclease s...
Entire | Name: HSV-1 DNA polymerase-processivity factor complex in exonuclease state with 1-bp DNA mismatch |
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Components |
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-Supramolecule #1: HSV-1 DNA polymerase-processivity factor complex in exonuclease s...
Supramolecule | Name: HSV-1 DNA polymerase-processivity factor complex in exonuclease state with 1-bp DNA mismatch type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: DNA polymerase-processivity factor
Supramolecule | Name: DNA polymerase-processivity factor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Human alphaherpesvirus 1 strain KOS |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: DNA polymerase catalytic subunit
Macromolecule | Name: DNA polymerase catalytic subunit / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human alphaherpesvirus 1 strain KOS |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MFSGGGGPLS PGGKSAARAA SGFFAPAGPR GASRGPPPCL RQNFYNPYLA PVGTQQKPTG PTQRHTYYSE CDEFRFIAPR VLDEDAPPE KRAGVHDGHL KRAPKVYCGG DERDVLRVGS GGFWPRRSRL WGGVDHAPAG FNPTVTVFHV YDILENVEHA Y GMRAAQFH ...String: MFSGGGGPLS PGGKSAARAA SGFFAPAGPR GASRGPPPCL RQNFYNPYLA PVGTQQKPTG PTQRHTYYSE CDEFRFIAPR VLDEDAPPE KRAGVHDGHL KRAPKVYCGG DERDVLRVGS GGFWPRRSRL WGGVDHAPAG FNPTVTVFHV YDILENVEHA Y GMRAAQFH ARFMDAITPT GTVITLLGLT PEGHRVAVHV YGTRQYFYMN KEEVDRHLQC RAPRDLCERM AAALRESPGA SF RGISADH FEAEVVERTD VYYYETRPAL FYRVYVRSGR VLSYLCDNFC PAIKKYEGGV DATTRFILDN PGFVTFGWYR LKP GRNNTL AQPRAPMAFG TSSDVEFNCT ADNLAIEGGM SDLPAYKLMC FDIECKAGGE DELAFPVAGH PEDLVIQISC LLYD LSTTA LEHVLLFSLG SCDLPESHLN ELAARGLPTP VVLEFDSEFE MLLAFMTLVK QYGPEFVTGY NIINFDWPFL LAKLT DIYK VPLDGYGRMN GRGVFRVWDI GQSHFQKRSK IKVNGMVNID MYGIITDKIK LSSYKLNAVA EAVLKDKKKD LSYRDI PAY YAAGPAQRGV IGEYCIQDSL LVGQLFFKFL PHLELSAVAR LAGINITRTI YDGQQIRVFT CLLRLADQKG FILPDTQ GR FRGAGGEAPK RPAAAREDEE RPEEEGEDED EREEGGGERE PEGARETAGR HVGYQGARVL DPTSGFHVNP VVVFDFAS L YPSIIQAHNL CFSTLSLRAD AVAHLEAGKD YLEIEVGGRR LFFVKAHVRE SLLSILLRDW LAMRKQIRSR IPQSSPEEA VLLDKQQAAI KVVCNSVYGF TGVQHGLLPC LHVAATVTTI GREMLLATRE YVHARWAAFE QLLADFPEAA DMRAPGPYSM RIIYGDTDS IFVLCRGLTA AGLTAVGDKM ASHISRALFL PPIKLECEKT FTKLLLIAKK KYIGVIYGGK MLIKGVDLVR K NNCAFINR TSRALVDLLF YDDTVSGAAA ALAERPAEEW LARPLPEGLQ AFGAVLVDAH RRITDPERDI QDFVLTAELS RH PRAYTNK RLAHLTVYYK LMARRAQVPS IKDRIPYVIV AQTREVEETV ARLAALRELD AAAPGDEPAP PAALPSPAKR PRE TPSPAD PPGGASKPRK LLVSELAEDP AYAIAHGVAL NTDYYFSHLL GAACVTFKAL FGNNAKITES LLKRFIPEVW HPPD DVAAR LRTAGFGAVG AGATAEETRR MLHRAFDTLA |
-Macromolecule #2: Primer DNA
Macromolecule | Name: Primer DNA / type: dna / ID: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Sequence | String: GCCACTACGA CACCTTGATC GCCTCGCAGC CGTCCAACCA ACTC(DRG) |
-Macromolecule #3: Template DNA
Macromolecule | Name: Template DNA / type: dna / ID: 3 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Sequence | String: ATTTGCTGAC CTTTGTTCTG GGTGAGTTGG TTGGACGGCT GCGAGGCGAT CAAGGTGTCG TAGTGGC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | |||||||||||||||
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Buffer | pH: 7.8 Component:
Details: 20mM HEPES pH7.8, 150mM NaCl, 5mM CaCl2, 2mM DTT | |||||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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