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Yorodumi- EMDB-16907: HSV-1 DNA polymerase-processivity factor complex in halted elonga... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16907 | |||||||||
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Title | HSV-1 DNA polymerase-processivity factor complex in halted elongation state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA / Polymerase / Complex / TRANSFERASE | |||||||||
Function / homology | Function and homology information DNA polymerase activity / DNA polymerase complex / 5'-3' exonuclease activity / bidirectional double-stranded viral DNA replication / ribonuclease H / DNA polymerase processivity factor activity / RNA-DNA hybrid ribonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...DNA polymerase activity / DNA polymerase complex / 5'-3' exonuclease activity / bidirectional double-stranded viral DNA replication / ribonuclease H / DNA polymerase processivity factor activity / RNA-DNA hybrid ribonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / host cell nucleus / DNA binding Similarity search - Function | |||||||||
Biological species | Human alphaherpesvirus 1 strain KOS / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.46 Å | |||||||||
Authors | Gustavsson E / Grunewald K / Elias P / Hallberg BM | |||||||||
Funding support | Sweden, Germany, 2 items
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Citation | Journal: To Be Published Title: Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM Authors: Gustavsson E / Grunewald K / Elias P / Hallberg BM | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16907.map.gz | 3.1 MB | EMDB map data format | |
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Header (meta data) | emd-16907-v30.xml emd-16907.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
Images | emd_16907.png | 96.8 KB | ||
Masks | emd_16907_msk_1.map | 307.5 MB | Mask map | |
Filedesc metadata | emd-16907.cif.gz | 7.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16907 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16907 | HTTPS FTP |
-Related structure data
Related structure data | 8oj7MC 8oj6C 8ojaC 8ojbC 8ojcC 8ojdC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16907.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16907_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HSV-1 DNA polymerase-processivity factor complex in halted elonga...
Entire | Name: HSV-1 DNA polymerase-processivity factor complex in halted elongation state |
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Components |
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-Supramolecule #1: HSV-1 DNA polymerase-processivity factor complex in halted elonga...
Supramolecule | Name: HSV-1 DNA polymerase-processivity factor complex in halted elongation state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Human alphaherpesvirus 1 strain KOS |
-Macromolecule #1: DNA polymerase catalytic subunit
Macromolecule | Name: DNA polymerase catalytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase |
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Source (natural) | Organism: Human alphaherpesvirus 1 strain KOS |
Molecular weight | Theoretical: 136.683844 KDa |
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 UniProtKB: DNA polymerase catalytic subunit |
-Macromolecule #2: DNA polymerase processivity factor
Macromolecule | Name: DNA polymerase processivity factor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human alphaherpesvirus 1 strain KOS |
Molecular weight | Theoretical: 51.207969 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MTDSPGGVAP ASPVEDASDA SLGQPEEGAP CQVVLQGAEL NGILQAFAPL RTSLLDSLLV MGDRGILIHN TIFGEQVFLP LEHSQFSRY RWRGPTAAFL SLVDQKRSLL SVFRANQYPD LRRVELAITG QAPFRTLVQR IWTTTSDGEA VELASETLMK R ELTSFVVL ...String: MTDSPGGVAP ASPVEDASDA SLGQPEEGAP CQVVLQGAEL NGILQAFAPL RTSLLDSLLV MGDRGILIHN TIFGEQVFLP LEHSQFSRY RWRGPTAAFL SLVDQKRSLL SVFRANQYPD LRRVELAITG QAPFRTLVQR IWTTTSDGEA VELASETLMK R ELTSFVVL VPQGTPDVQL RLTRPQLTKV LNATGADSAT PTTFELGVNG KFSVFTTSTC VTFAAREEGV SSSTSTQVQI LS NALTKAG QAAANAKTVY GENTHRTFSV VVDDCSMRAV LRRLQVGGGT LKFFLTTPVP SLCVTATGPN AVSAVFLLKP QKI CLDWLG HSQGSPSAGS SASRASGSEP TDSQDSASDA VSHGDPEDLD GAARAGEAGA LHACPMPSST TRVTPTTKRG RSGG EDARA DTALKKPKTG SPTAPPPADP VPLDTEDDSD AADGTAARPA APDARSGSRY ACYFRDLPTG EASPGAFSAF RGGPQ TPYG FGFP UniProtKB: DNA polymerase processivity factor |
-Macromolecule #3: DNA (53-MER)
Macromolecule | Name: DNA (53-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 16.081343 KDa |
Sequence | String: (DG)(DC)(DC)(DA)(DC)(DT)(DA)(DC)(DG)(DA) (DC)(DA)(DC)(DC)(DT)(DT)(DG)(DA)(DT)(DC) (DG)(DC)(DC)(DT)(DC)(DG)(DC)(DA)(DG) (DC)(DC)(DG)(DT)(DC)(DC)(DA)(DA)(DC)(DC) (DA) (DA)(DC)(DT)(DC)(DA)(DA) ...String: (DG)(DC)(DC)(DA)(DC)(DT)(DA)(DC)(DG)(DA) (DC)(DA)(DC)(DC)(DT)(DT)(DG)(DA)(DT)(DC) (DG)(DC)(DC)(DT)(DC)(DG)(DC)(DA)(DG) (DC)(DC)(DG)(DT)(DC)(DC)(DA)(DA)(DC)(DC) (DA) (DA)(DC)(DT)(DC)(DA)(DA)(DT)(DT) (DA)(DG)(DA)(DA)(DOC) |
-Macromolecule #4: DNA (67-MER)
Macromolecule | Name: DNA (67-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 20.845285 KDa |
Sequence | String: (DA)(DT)(DT)(DT)(DG)(DC)(DT)(DG)(DA)(DC) (DC)(DT)(DT)(DT)(DG)(DT)(DT)(DC)(DT)(DA) (DA)(DT)(DT)(DG)(DA)(DG)(DT)(DT)(DG) (DG)(DT)(DT)(DG)(DG)(DA)(DC)(DG)(DG)(DC) (DT) (DG)(DC)(DG)(DA)(DG)(DG) ...String: (DA)(DT)(DT)(DT)(DG)(DC)(DT)(DG)(DA)(DC) (DC)(DT)(DT)(DT)(DG)(DT)(DT)(DC)(DT)(DA) (DA)(DT)(DT)(DG)(DA)(DG)(DT)(DT)(DG) (DG)(DT)(DT)(DG)(DG)(DA)(DC)(DG)(DG)(DC) (DT) (DG)(DC)(DG)(DA)(DG)(DG)(DC)(DG) (DA)(DT)(DC)(DA)(DA)(DG)(DG)(DT)(DG)(DT) (DC)(DG) (DT)(DA)(DG)(DT)(DG)(DG)(DC) |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Macromolecule | Name: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: DTP |
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Molecular weight | Theoretical: 491.182 Da |
Chemical component information | ChemComp-DTP: |
-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 MgCl2, 2mM DTT | |||||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. | |||||||||||||||
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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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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.3) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Details: cryoSPARC Non-uniform refinement / Number images used: 213621 |