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- EMDB-49585: Composite structure of HSV-1 helicase-primase in complex with a f... -

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Basic information

Entry
Database: EMDB / ID: EMD-49585
TitleComposite structure of HSV-1 helicase-primase in complex with a forked DNA
Map dataComposite map of HSV-1 helicase-primase in complex with a forked DNA
Sample
  • Complex: HSV-1 helicase-primase in complex with a forked DNA
    • Protein or peptide: DNA replication helicase
    • Protein or peptide: DNA primase
    • Protein or peptide: DNA helicase/primase complex-associated protein
    • DNA: DNA (5'-D(P*TP*AP*CP*AP*TP*AP*A)-3')
  • Ligand: ZINC ION
KeywordsDNA replication / HSV-1 helicase-primase / VIRAL PROTEIN / Transferase-Hydrolase-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA-directed RNA polymerase activity / DNA replication / hydrolase activity / host cell nucleus / zinc ion binding / 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
DNA replication helicase / DNA helicase/primase complex-associated protein / DNA primase
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain 17 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHe Q / Baranovskiy AG / Morstadt LM / Babayeva ND / Lim C / Tahirov TH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM152032 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM150023 United States
CitationJournal: Sci Adv / Year: 2025
Title: Structural basis of herpesvirus helicase-primase inhibition by pritelivir and amenamevir.
Authors: Andrey G Baranovskiy / Qixiang He / Yoshiaki Suwa / Lucia M Morstadt / Nigar D Babayeva / Ci Ji Lim / Tahir H Tahirov /
Abstract: Widespread herpesvirus infections are associated with various diseases. DNA replication of human herpes simplex virus type 1 (HSV-1) requires a helicase-primase (HP) complex of three core proteins: ...Widespread herpesvirus infections are associated with various diseases. DNA replication of human herpes simplex virus type 1 (HSV-1) requires a helicase-primase (HP) complex of three core proteins: UL5, UL52, and UL8. This complex unwinds viral DNA and synthesizes primers for DNA replication, making it an attractive antiviral target. Although HP inhibitors pritelivir and amenamevir were identified through screening, their binding mechanisms remain unclear. Here, we report cryo-electron microscopy structures of HSV-1 HP bound to a forked DNA template alone and in complex with pritelivir or amenamevir. The structures reveal a bilobed architecture highlighting HP coordinated action at the replication fork and providing a structural basis for HP inhibition by illustrating precisely how pritelivir and amenamevir block helicase activity. Data lay a solid foundation for the development of improved antiviral therapies.
History
DepositionMar 5, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49585.png

Downloads & links

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Map

FileDownload / File: emd_49585.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of HSV-1 helicase-primase in complex with a forked DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.64046484 - 1.0813934
Average (Standard dev.)0.00036450423 (±0.01771336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : HSV-1 helicase-primase in complex with a forked DNA

EntireName: HSV-1 helicase-primase in complex with a forked DNA
Components
  • Complex: HSV-1 helicase-primase in complex with a forked DNA
    • Protein or peptide: DNA replication helicase
    • Protein or peptide: DNA primase
    • Protein or peptide: DNA helicase/primase complex-associated protein
    • DNA: DNA (5'-D(P*TP*AP*CP*AP*TP*AP*A)-3')
  • Ligand: ZINC ION

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Supramolecule #1: HSV-1 helicase-primase in complex with a forked DNA

SupramoleculeName: HSV-1 helicase-primase in complex with a forked DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: HSV-1 helicase-primase in complex with a forked DNAsovled using cryo-EM single-particle analysis
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: DNA replication helicase

MacromoleculeName: DNA replication helicase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 95.760805 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GRAEAFLNFT SMHGVQPILK RIRELSQQQL DGAQVPHLQW FRDVAALESP AGLPLREFPF AVYLITGNAG SGKSTCVQTI NEVLDCVVT GATRIAAQNM YAKLSGAFLS RPINTIFHEF GFRGNHVQAQ LGQYPYTLTS NPASLEDLQR RDLTYYWEVI L DLTKRALA ...String:
GRAEAFLNFT SMHGVQPILK RIRELSQQQL DGAQVPHLQW FRDVAALESP AGLPLREFPF AVYLITGNAG SGKSTCVQTI NEVLDCVVT GATRIAAQNM YAKLSGAFLS RPINTIFHEF GFRGNHVQAQ LGQYPYTLTS NPASLEDLQR RDLTYYWEVI L DLTKRALA ASGGEELRNE FRALAALERT LGLAEGALTR LAPATHGALP AFTRSNVIVI DEAGLLGRHL LTAVVYCWWM IN ALYHTPQ YAARLRPVLV CVGSPTQTAS LESTFEHQKL RCSVRQSENV LTYLICNRTL REYARLSYSW AIFINNKRCV EHE FGNLMK VLEYGLPITE EHMQFVDRFV VPENYITNPA NLPGWTRLFS SHKEVSAYMA KLHAYLKVTR EGEFVVFTLP VLTF VSVKE FDEYRRLTHQ PGLTIEKWLT ANASRITNYS QSQDQDAGHM RCEVHSKQQL VVARNDVTYV LNSQIAVTAR LRKLV FGFS GTFRAFEAVL RDDSFVKTQG ETSVEFAYRF LSRLIFSGLI SFYNFLQRPG LDATQRTLAY ARMGELTAEI LSLRPK SSG VPTQASVMAD AGAPGERAFD FKQLGPRDGG PDDFPDDDLD VIFAGLDEQQ LDVFYCHYTP GEPETTAAVH TQFALLK RA FLGRFRILQE LFGEAFEVAP FSTYVDNVIF RGCEMLTGSP RGGLMSVALQ TDNYTLMGYT YARVFAFADE LRRRHATA N VAELLEEAPL PYVVLRDQHG FMSVVNTNIS EFVESIDSTE LAMAINADYG ISSKLAMTIT RSQGLSLDKV AICFTPGNL RLNSAYVAMS RTTSSEFLRM NLNPLRERHE RDDVISEHIL SALRDPNVVI VY

UniProtKB: DNA replication helicase

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Macromolecule #2: DNA primase

MacromoleculeName: DNA primase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 114.558562 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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: DNA primase

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Macromolecule #3: DNA helicase/primase complex-associated protein

MacromoleculeName: DNA helicase/primase complex-associated protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 80.005664 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 #4: DNA (5'-D(P*TP*AP*CP*AP*TP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*TP*AP*CP*AP*TP*AP*A)-3') / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.56493 KDa
SequenceString:
(DC)(DC)(DA)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DT)(DA)(DC)(DA)(DT)(DA)(DA)(DT)(DA)(DC) (DA)(DT)(DA)(DC)(DA)

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration4.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
100.0 mMKClpotassium chloride
0.5 percentGlycerolGlycerol
2.0 mMDTTdithiothreitol
4.0 mMCHAPSOCHAPSO

Details: CHAPSO is made fresh at 80 mM before being added to the sample at a final concentration of 4 mM immediately before vitrification
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12555 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4446980
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: From Cryosparc
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 431843
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9nnp:
Composite structure of HSV-1 helicase-primase in complex with a forked DNA

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