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- EMDB-72789: HSV Helicase-primase complex bound to amenamevir -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72789
TitleHSV Helicase-primase complex bound to amenamevir
Map data
Sample
  • Complex: HSV helicase-primase complex bound to amenamevir
    • DNA: DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')
    • Protein or peptide: UL52
    • Protein or peptide: UL5
    • Protein or peptide: UL8
  • Ligand: ZINC ION
  • Ligand: Amenamevir
KeywordsHSV / helicase-primase / HPI / VIRAL PROTEIN
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / helicase activity / DNA-directed RNA polymerase activity / DNA replication / hydrolase activity / host cell nucleus / ATP binding
Similarity search - Function
DNA replication helicase domain / DNA helicase/primase complex-associated protein / DNA replication helicase, Herpesvirus / Herpesvirus DNA helicase/primase complex associated protein / Helicase / DNA primase / Herpesviridae UL52/UL70 DNA primase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Helicase-primase helicase subunit / Helicase-primase primase subunit / DNA helicase/primase complex-associated protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain R-15
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsYu Z / Abraham J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mechanisms of HSV replisome assembly and targeting by helicase?primase inhibitors
Authors: Yu Z / Abraham J
History
DepositionSep 19, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72789.png

Downloads & links

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Map

FileDownload / File: emd_72789.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0018182711 - 1.8993686
Average (Standard dev.)0.0014716749 (±0.026510507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 292.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : HSV helicase-primase complex bound to amenamevir

EntireName: HSV helicase-primase complex bound to amenamevir
Components
  • Complex: HSV helicase-primase complex bound to amenamevir
    • DNA: DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')
    • Protein or peptide: UL52
    • Protein or peptide: UL5
    • Protein or peptide: UL8
  • Ligand: ZINC ION
  • Ligand: Amenamevir

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Supramolecule #1: HSV helicase-primase complex bound to amenamevir

SupramoleculeName: HSV helicase-primase complex bound to amenamevir / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15

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Macromolecule #1: DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')

MacromoleculeName: DNA (5'-D(*TP*TP*TP*TP*TP*T)-3') / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 1.780199 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #2: UL52

MacromoleculeName: UL52 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 114.558562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGQEDGNRGE RRAAGTPVEV TALYATDGCV ITSSIALLTN SLLGAEPVYI FSYDAYTHDG RADGPTEQDR FEESRALYQA SGGLNGDSF RVTFCLLGTE VGGTHQARGR TRPMFVCRFE RADDVAALQD ALAHGTPLQP DHIAATLDAE ATFALHANMI L ALTVAINN ...String:
MGQEDGNRGE RRAAGTPVEV TALYATDGCV ITSSIALLTN SLLGAEPVYI FSYDAYTHDG RADGPTEQDR FEESRALYQA SGGLNGDSF RVTFCLLGTE VGGTHQARGR TRPMFVCRFE RADDVAALQD ALAHGTPLQP DHIAATLDAE ATFALHANMI L ALTVAINN ASPRTGRDAA AAQYDQGASL RSLVGRTSLG QRGLTTLYVH HEVRVLAAYR RAYYGSAQSP FWFLSKFGPD EK SLVLTTR YYLLQAQRLG GAGATYDLQA IKDICATYAI PHAPRPDTVS AASLTSFAAI TRFCCTSQYA RGAAAAGFPL YVE RRIAAD VRETSALEKF ITHDRSCLRV SDREFITYIY LAHFECFSPP RLATHLRAVT THDPNPAAST EQPSPLGREA VEQF FCHVR AQLNIGEYVK HNVTPRETVL DGDTAKAYLR ARTYAPGALT PAPAYCGAVD SATKMMGRLA DAEKLLVPRG WPAFA PASP GEDTAGGTPP PQTCGIVKRL LRLAATEQQG PTPPAIAALI RNAAVQTPLP VYRISMVPTG QAFAALAWDD WARITR DAR LAEAVVSAEA AAHPDHGALG RRLTDRIRAQ GPVMPPGGLD AGGQMYVNRN EIFNGALAIT NIILDLDIAL KEPVPFR RL HEALGHFRRG ALAAVQLLFP AARVDPDAYP CYFFKSACRP GPASVGSGSG LGNDDDGDWF PCYDDAGDEE WAEDPGAM D TSHDPPDDEV AYFDLCHEVG PTAEPRETDS PVCSCTDKIG LRVCMPVPAP YVVHGSLTMR GVARVIQQAV LLDRDFVEA IGSYVKNFLL IDTGVYAHGH SLRLPYFAKI APDGPACGRL LPVFVIPPAC KDVPAFVAAH ADPRRFHFHA PPTYLASPRE IRVLHSLGG DYVSFFERKA SRNALEHFGR RETLTEVLGR YNVQPDAGGT VEGFASELLG RIVACIETHF PEHAGEYQAV S VRRAVSKD DWVLLQLVPV RGTLQQSLSC LRFKHGRASR ATARTFVALS VGANNRLCVS LCQQCFAAKC DSNRLHTLFT ID AGTPCSP SVPCSTSQPS S

UniProtKB: Helicase-primase primase subunit

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Macromolecule #3: UL5

MacromoleculeName: UL5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 98.823242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAGGERQL DGQKPGPPHL QQPGDRPAVP GRAEAFLNFT SMHGVQPILK RIRELSQQQL DGAQVPHLQW FRDVAALESP AGLPLREFP FAVYLITGNA GSGKSTCVQT INEVLDCVVT GATRIAAQNM YAKLSGAFLS RPINTIFHEF GFRGNHVQAQ L GQYPYTLT ...String:
MAAAGGERQL DGQKPGPPHL QQPGDRPAVP GRAEAFLNFT SMHGVQPILK RIRELSQQQL DGAQVPHLQW FRDVAALESP AGLPLREFP FAVYLITGNA GSGKSTCVQT INEVLDCVVT GATRIAAQNM YAKLSGAFLS RPINTIFHEF GFRGNHVQAQ L GQYPYTLT SNPASLEDLQ RRDLTYYWEV ILDLTKRALA ASGGEELRNE FRALAALERT LGLAEGALTR LAPATHGALP AF TRSNVIV IDEAGLLGRH LLTAVVYCWW MINALYHTPQ YAARLRPVLV CVGSPTQTAS LESTFEHQKL RCSVRQSENV LTY LICNRT LREYARLSYS WAIFINNKRC VEHEFGNLMK VLEYGLPITE EHMQFVDRFV VPENYITNPA NLPGWTRLFS SHKE VSAYM AKLHAYLKVT REGEFVVFTL PVLTFVSVKE FDEYRRLTHQ PGLTIEKWLT ANASRITNYS QSQDQDAGHM RCEVH SKQQ LVVARNDVTY VLNSQIAVTA RLRKLVFGFS GTFRAFEAVL RDDSFVKTQG ETSVEFAYRF LSRLIFSGLI SFYNFL QRP GLDATQRTLA YARMGELTAE ILSLRPKSSG VPTQASVMAD AGAPGERAFD FKQLGPRDGG PDDFPDDDLD VIFAGLD EQ QLDVFYCHYT PGEPETTAAV HTQFALLKRA FLGRFRILQE LFGEAFEVAP FSTYVDNVIF RGCEMLTGSP RGGLMSVA L QTDNYTLMGY TYARVFAFAD ELRRRHATAN VAELLEEAPL PYVVLRDQHG FMSVVNTNIS EFVESIDSTE LAMAINADY GISSKLAMTI TRSQGLSLDK VAICFTPGNL RLNSAYVAMS RTTSSEFLRM NLNPLRERHE RDDVISEHIL SALRDPNVVI VY

UniProtKB: Helicase-primase helicase subunit

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Macromolecule #4: UL8

MacromoleculeName: UL8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Molecular weightTheoretical: 80.005664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDTADIVWVE ESVSAITLYA VWLPPRAREY FHALVYFVCR NAAGEGRARF AEVSVTATEL RDFYGSADVS VQAVVAAARA ATTPAASPL EPLENPTLWR ALYACVLAAL ERQTGPVALF APLRIGSDPR TGLVVKVERA SWGPPAAPRA ALLVAEANID I DPMALAAR ...String:
MDTADIVWVE ESVSAITLYA VWLPPRAREY FHALVYFVCR NAAGEGRARF AEVSVTATEL RDFYGSADVS VQAVVAAARA ATTPAASPL EPLENPTLWR ALYACVLAAL ERQTGPVALF APLRIGSDPR TGLVVKVERA SWGPPAAPRA ALLVAEANID I DPMALAAR VAEHPDARLA WARLAAIRDT PQCASAASLT VNITTGTALF AREYQTLAFP PIKKEGAFGD LVEVCEVGLR PR GHPQRVT ARVLLPRDYD YFVSAGEKFS APALVALFRQ WHTTVHAAPG ALAPVFAFLG PEFEVRGGPV PYFAVLGFPG WPT FTVPAT AESARDLVRG AAAAYAALLG AWPAVGARVV LPPRAWPGVA SAAAGCLLPA VREAVARWHP ATKIIQLLDP PAAV GPVWT ARFCFPGLRA QLLAALADLG GSGLADPHGR TGLARLDALV VAAPSEPWAG AVLERLVPDT CNACPALRQL LGGVM AAVC LQIEETASSV KFAVCGGDGG AFWGVFNVDP QDADAASGVI EDARRAIETA VGAVLRANAV RLRHPLCLAL EGVYTH AVA WSQAGVWFWN SRDNTDHLGG FPLRGPAYTT AAGVVRDTLR RVLGLTTACV PEEDALTARG LMEDACDRLI LDAFNKR LD AEYWSVRVSP FEASDPLPPT AFRGGALLDA EHYWRRVVRV CPGGGESVGV PVDLYPRPLV LPPVDCAHHL REILREIE L VFTGVLAGVW GEGGKFVYPF DDKMSFLFA

UniProtKB: DNA helicase/primase complex-associated protein

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: Amenamevir

MacromoleculeName: Amenamevir / type: ligand / ID: 6 / Number of copies: 1 / Formula: A1BXD
Molecular weightTheoretical: 482.552 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 340000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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