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- EMDB-65163: herpes simplex virus type 1 helicase-primase structure in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-65163
Titleherpes simplex virus type 1 helicase-primase structure in complex with ssDNA, ADP and magnesium ion
Map datacomposite map
Sample
  • Complex: HSV-1 helicase-primase in complex with ssDNA, ADP and magnesium
    • Protein or peptide: DNA replication helicase
    • Protein or peptide: Helicase-primase subunit
    • Protein or peptide: DNA primase
    • DNA: DNA (44-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsherpes simplex virus type 1 / helicase / primase / UL5 / UL52 / UL8 / DNA replication / Helicase superfamily I / SF1 / REPLICATION/DNA / REPLICATION-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / viral genome 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
Helicase-primase subunit / DNA replication helicase / DNA primase
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain 17 / ssDNA virus sp.
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWu YQ / Jiang ZY / Chen XL / Zheng ZY / Dong CJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Cell Discov / Year: 2025
Title: Structural and mechanistic insights into the herpes simplex virus type 1 helicase-primase primosome.
Authors: Yaqi Wu / Ziyi Jiang / Xiaoling Chen / Danyang Li / Zhengyu Zhang / Changjiang Dong /
Abstract: DNA unwinding and primer synthesis are fundamental processes in genome replication. The human herpes simplex virus type 1 (HSV-1) helicase-primase forms a unique heterotrimeric primosome that is ...DNA unwinding and primer synthesis are fundamental processes in genome replication. The human herpes simplex virus type 1 (HSV-1) helicase-primase forms a unique heterotrimeric primosome that is essential for viral DNA unwinding and primer synthesis and represents an ideal drug target. However, its molecular mechanism remains poorly understood. Here we report the cryo-electron microscopic structure of the primosome in complex with single-stranded DNA, ADP and Mg to 3.47 Å resolution, which reveals that the primosome forms an unprecedented architecture in a fully open DNA binding groove between the helicase domains 1A and 2A-2B and that the primase subunit UL52 interacts extensively with the helicase subunit UL5 and accessory protein subunit UL8. Integrating mutagenesis, biochemical assays, structural analysis and 3D variability display analysis, we have identified the active sites of the ATPase, helicase and primase and critical interfaces between UL52, UL5 and UL8. Our work suggests that the primosome unwinds and translocates DNA via bidirectional rotation, and proposes a mechanistic model for DNA-dependent ATPase activation and alternating activity between helicase and primase. Herpesviridae family viruses pose significant threats to human health worldwide, and this trimeric assembly of primosomes is conserved. Our work provides a framework for understanding replication mechanisms across related viruses and for the rational design of broad-spectrum antivirals.
History
DepositionJun 26, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65163.png

Downloads & links

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Map

FileDownload / File: emd_65163.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 480 pix.
= 403.2 Å		0.84 Å/pix.
x 480 pix.
= 403.2 Å		0.84 Å/pix.
x 480 pix.
= 403.2 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: 0.1
Minimum - Maximum-0.43872505 - 0.84031105
Average (Standard dev.)0.00445266 (±0.015508432)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 403.19998 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 ssDNA, ADP and magnesium

EntireName: HSV-1 helicase-primase in complex with ssDNA, ADP and magnesium
Components
  • Complex: HSV-1 helicase-primase in complex with ssDNA, ADP and magnesium
    • Protein or peptide: DNA replication helicase
    • Protein or peptide: Helicase-primase subunit
    • Protein or peptide: DNA primase
    • DNA: DNA (44-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: HSV-1 helicase-primase in complex with ssDNA, ADP and magnesium

SupramoleculeName: HSV-1 helicase-primase in complex with ssDNA, ADP and magnesium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human alphaherpesvirus 1 strain 17

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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: 101.903492 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBachsGCA1 (others)
SequenceString: MHHHHHHHHD YDIPTTENLY FQGADMAAAG GERQLDGQKP GPPHLQQPGD RPAVPGRAEA FLNFTSMHGV QPILKRIREL SQQQLDGAQ VPHLQWFRDV AALESPAGLP LREFPFAVYL ITGNAGSGKS TCVQTINEVL DCVVTGATRI AAQNMYAKLS G AFLSRPIN ...String:
MHHHHHHHHD YDIPTTENLY FQGADMAAAG GERQLDGQKP GPPHLQQPGD RPAVPGRAEA FLNFTSMHGV QPILKRIREL SQQQLDGAQ VPHLQWFRDV AALESPAGLP LREFPFAVYL ITGNAGSGKS TCVQTINEVL DCVVTGATRI AAQNMYAKLS G AFLSRPIN TIFHEFGFRG NHVQAQLGQY PYTLTSNPAS LEDLQRRDLT YYWEVILDLT KRALAASGGE ELRNEFRALA AL ERTLGLA EGALTRLAPA THGALPAFTR SNVIVIDEAG LLGRHLLTAV VYCWWMINAL YHTPQYAARL RPVLVCVGSP TQT ASLEST FEHQKLRCSV RQSENVLTYL ICNRTLREYA RLSYSWAIFI NNKRCVEHEF GNLMKVLEYG LPITEEHMQF VDRF VVPEN YITNPANLPG WTRLFSSHKE VSAYMAKLHA YLKVTREGEF VVFTLPVLTF VSVKEFDEYR RLTHQPGLTI EKWLT ANAS RITNYSQSQD QDAGHMRCEV HSKQQLVVAR NDVTYVLNSQ IAVTARLRKL VFGFSGTFRA FEAVLRDDSF VKTQGE TSV EFAYRFLSRL IFSGLISFYN FLQRPGLDAT QRTLAYARMG ELTAEILSLR PKSSGVPTQA SVMADAGAPG ERAFDFK QL GPRDGGPDDF PDDDLDVIFA GLDEQQLDVF YCHYTPGEPE TTAAVHTQFA LLKRAFLGRF RILQELFGEA FEVAPFST Y VDNVIFRGCE MLTGSPRGGL MSVALQTDNY TLMGYTYARV FAFADELRRR HATANVAELL EEAPLPYVVL RDQHGFMSV VNTNISEFVE SIDSTELAMA INADYGISSK LAMTITRSQG LSLDKVAICF TPGNLRLNSA YVAMSRTTSS EFLRMNLNPL RERHERDDV ISEHILSALR DPNVVIVY

UniProtKB: DNA replication helicase

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Macromolecule #2: Helicase-primase subunit

MacromoleculeName: Helicase-primase subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 83.085953 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBachsGCA1 (others)
SequenceString: MHHHHHHHHD YDIPTTENLY FQGADMDTAD IVWVEESVSA ITLYAVWLPP RAREYFHALV YFVCRNAAGE GRARFAEVSV TATELRDFY GSADVSVQAV VAAARAATTP AASPLEPLEN PTLWRALYAC VLAALERQTG PVALFAPLRI GSDPRTGLVV K VERASWGP ...String:
MHHHHHHHHD YDIPTTENLY FQGADMDTAD IVWVEESVSA ITLYAVWLPP RAREYFHALV YFVCRNAAGE GRARFAEVSV TATELRDFY GSADVSVQAV VAAARAATTP AASPLEPLEN PTLWRALYAC VLAALERQTG PVALFAPLRI GSDPRTGLVV K VERASWGP PAAPRAALLV AEANIDIDPM ALAARVAEHP DARLAWARLA AIRDTPQCAS AASLTVNITT GTALFAREYQ TL AFPPIKK EGAFGDLVEV CEVGLRPRGH PQRVTARVLL PRDYDYFVSA GEKFSAPALV ALFRQWHTTV HAAPGALAPV FAF LGPEFE VRGGPVPYFA VLGFPGWPTF TVPATAESAR DLVRGAAAAY AALLGAWPAV GARVVLPPRA WPGVASAAAG CLLP AVREA VARWHPATKI IQLLDPPAAV GPVWTARFCF PGLRAQLLAA LADLGGSGLA DPHGRTGLAR LDALVVAAPS EPWAG AVLE RLVPDTCNAC PALRQLLGGV MAAVCLQIEE TASSVKFAVC GGDGGAFWGV FNVDPQDADA ASGVIEDARR AIETAV GAV LRANGLRLRH PLCLALEGVY THAVAWSQAG VWFWNSRDNT DHLGGFPLRG PAYTTAAGVV RDTLRRVLGL TTACVPE ED ALTARGLMED ACDRLILDAF NKRLDAEYWS VRVSPFEASD PLPPTAFRGG ALLDAEHYWR RVVRVCPGGG ESVGVPVD L YPRPLVLPPV DCAHHLREIL REIELVFTGV LAGVWGEGGK FVYPFDDKMS FLFA

UniProtKB: Helicase-primase subunit

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Macromolecule #3: DNA primase

MacromoleculeName: DNA primase / type: protein_or_peptide / ID: 3 / 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: Insect expression vector pBlueBachsGCA1 (others)
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 #4: DNA (44-MER)

MacromoleculeName: DNA (44-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: ssDNA virus sp.
Molecular weightTheoretical: 13.402571 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DC)(DT)(DG) (DG)(DT)(DC)(DA)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 35958
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.0)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9vlq:
herpes simplex virus type 1 helicase-primase structure in complex with ssDNA, ADP and magnesium ion

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