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- EMDB-61289: Herpes simplex virus type 1 polymerase machinery in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-61289
TitleHerpes simplex virus type 1 polymerase machinery in complex with duplex DNA, acyclovir triphosphate and calcium ions
Map dataHerpes simplex virus type 1 DNA polymerase machinery in complex with acyclovir triphosphate and calcium ions
Sample
  • Complex: Herpes simplex virus type 1 DNA replication machinery in complex DNA duplex and dGTP
    • Protein or peptide: DNA polymerase
    • Protein or peptide: DNA polymerase processivity factor
    • DNA: DNA (27-MER)
    • DNA: DNA (5'-D(*AP*GP*GP*CP*CP*AP*TP*AP*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
  • Ligand: CALCIUM ION
  • Ligand: ACYCLOVIR TRIPHOSPHATE
KeywordsHerpes simplex virus type 1 / HSV-1 / UL30 / UL42 / DNA replication holoenzyme / DNA replication machinery / acyclovir triphosphate / DNA / Calcium / REPLICATION
Function / homology
Function and homology information


DNA polymerase complex / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA polymerase processivity factor activity / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding ...DNA polymerase complex / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA polymerase processivity factor activity / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / host cell nucleus / DNA binding
Similarity search - Function
DNA polymerase processivity factor (UL42) / DNA polymerase processivity factor (UL42) / DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B ...DNA polymerase processivity factor (UL42) / DNA polymerase processivity factor (UL42) / DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / : / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA polymerase / DNA polymerase processivity factor
Similarity search - Component
Biological speciesHuman herpesvirus 1 (strain 17) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsWu YQ / Chen XL / Jiang ZY / Li DY / Zhang ZY / Dong CJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32250710142 China
CitationJournal: To Be Published
Title: Structural basis of herpes simplex type 1 virus DNA polymerase holoenzyme in DNA replication and acyclovir inhibition and proof-reading
Authors: Wu YQ / Chen XL / Jiang ZY / Li DY / Zhang ZY / Dong CJ
History
DepositionAug 24, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61289.png

Downloads & links

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Map

FileDownload / File: emd_61289.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHerpes simplex virus type 1 DNA polymerase machinery in complex with acyclovir triphosphate and calcium ions
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.61112046 - 0.94733053
Average (Standard dev.)-0.00008236393 (±0.02080376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_61289_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_61289_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Herpes simplex virus type 1 DNA replication machinery in complex ...

EntireName: Herpes simplex virus type 1 DNA replication machinery in complex DNA duplex and dGTP
Components
  • Complex: Herpes simplex virus type 1 DNA replication machinery in complex DNA duplex and dGTP
    • Protein or peptide: DNA polymerase
    • Protein or peptide: DNA polymerase processivity factor
    • DNA: DNA (27-MER)
    • DNA: DNA (5'-D(*AP*GP*GP*CP*CP*AP*TP*AP*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
  • Ligand: CALCIUM ION
  • Ligand: ACYCLOVIR TRIPHOSPHATE

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Supramolecule #1: Herpes simplex virus type 1 DNA replication machinery in complex ...

SupramoleculeName: Herpes simplex virus type 1 DNA replication machinery in complex DNA duplex and dGTP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human herpesvirus 1 (strain 17)

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Macromolecule #1: DNA polymerase

MacromoleculeName: DNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Human herpesvirus 1 (strain 17)
Molecular weightTheoretical: 136.683844 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBacmsGCA1 (others)
SequenceString: 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

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Macromolecule #2: DNA polymerase processivity factor

MacromoleculeName: DNA polymerase processivity factor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 (strain 17)
Molecular weightTheoretical: 54.288227 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBacmsGCA1His (others)
SequenceString: MHHHHHHHHD YDIPTTENLY FQGADMTDSP GGVAPASPVE DASDASLGQP EEGAPCQVVL QGAELNGILQ AFAPLRTSLL DSLLVMGDR GILIHNTIFG EQVFLPLEHS QFSRYRWRGP TAAFLSLVDQ KRSLLSVFRA NQYPDLRRVE LAITGQAPFR T LVQRIWTT ...String:
MHHHHHHHHD YDIPTTENLY FQGADMTDSP GGVAPASPVE DASDASLGQP EEGAPCQVVL QGAELNGILQ AFAPLRTSLL DSLLVMGDR GILIHNTIFG EQVFLPLEHS QFSRYRWRGP TAAFLSLVDQ KRSLLSVFRA NQYPDLRRVE LAITGQAPFR T LVQRIWTT TSDGEAVELA SETLMKRELT SFVVLVPQGT PDVQLRLTRP QLTKVLNATG ADSATPTTFE LGVNGKFSVF TT STCVTFA AREEGVSSST STQVQILSNA LTKAGQAAAN AKTVYGENTH RTFSVVVDDC SMRAVLRRLQ VGGGTLKFFL TTP VPSLCV TATGPNAVSA VFLLKPQKIC LDWLGHSQGS PSAGSSASRA SGSEPTDSQD SASDAVSHGD PEDLDGAARA GEAG ALHAC PMPSSTTRVT PTTKRGRSGG EDARADTALK KPKTGSPTAP PPADPVPLDT EDDSDAADGT AARPAAPDAR SGSRY ACYF RDLPTGEASP GAFSAFRGGP QTPYGFGFP

UniProtKB: DNA polymerase processivity factor

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Macromolecule #3: DNA (27-MER)

MacromoleculeName: DNA (27-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.421433 KDa
SequenceString:
(DA)(DA)(DT)(DC)(DG)(DT)(DA)(DG)(DG)(DG) (DG)(DA)(DA)(DG)(DG)(DA)(DT)(DC)(DG)(DT) (DA)(DT)(DG)(DG)(DC)(DC)(DT)

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Macromolecule #4: DNA (5'-D(*AP*GP*GP*CP*CP*AP*TP*AP*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*...

MacromoleculeName: DNA (5'-D(*AP*GP*GP*CP*CP*AP*TP*AP*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.921475 KDa
SequenceString:
(DA)(DG)(DG)(DC)(DC)(DA)(DT)(DA)(DC)(DG) (DA)(DT)(DC)(DC)(DT)(DT)(DC)(DC)(DC)(DC) (DT)(DA)(DC)

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: ACYCLOVIR TRIPHOSPHATE

MacromoleculeName: ACYCLOVIR TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: AVP
Molecular weightTheoretical: 465.144 Da
Chemical component information

ChemComp-AVP:
ACYCLOVIR TRIPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.4 mg/mL
BufferpH: 7.2
Details: 25 mM MOPS, pH 7.2, 150mM NaCl, 5% glycerol, 1mM tris(2-carboxyethyl) phosphine (TCEP)
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7luf


Details: PDB 7LUF and 1DML
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 678158
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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