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- EMDB-64481: The helicase-primase complex from HHV1 bound with ssDNA and pritelivir -

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Basic information

Entry
Database: EMDB / ID: EMD-64481
TitleThe helicase-primase complex from HHV1 bound with ssDNA and pritelivir
Map data3DFlex map
Sample
  • Complex: Helicase-primase complex from human herpesvirus 1
    • Complex: helicase
      • Protein or peptide: DNA replication helicase
    • Complex: primase
      • Protein or peptide: Ubiquitin-like protein SMT3,DNA primase
      • Protein or peptide: Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein
    • Complex: ssDNA
      • DNA: synthetic DNA
  • Ligand: Pritelivir
  • Ligand: ZINC ION
KeywordsHelicase / Primase / Inhibitor Complex / Herpesvirus / REPLICATION
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / bidirectional double-stranded viral DNA replication / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / helicase activity / condensed nuclear chromosome / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein tag activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA-directed RNA polymerase activity / DNA replication / hydrolase activity / host cell nucleus / zinc ion binding / ATP binding / identical protein binding / nucleus
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 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues ...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 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA replication helicase / DNA helicase/primase complex-associated protein / DNA primase / Small ubiquitin-related modifier
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 (Herpes simplex virus type 1) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsSato K / Kise Y / Hamada K / Nureki O / Sengoku T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: The helicase-primase complex from HHV1 bound with ssDNA and amenamevir
Authors: Sato K / Kise Y / Hamada K / Nureki O / Sengoku T
History
DepositionMay 2, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64481.png

Downloads & links

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Map

FileDownload / File: emd_64481.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3DFlex map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 200 pix.
= 249. Å		1.25 Å/pix.
x 200 pix.
= 249. Å		1.25 Å/pix.
x 200 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.09399238 - 0.15590602
Average (Standard dev.)0.00046077065 (±0.00491133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: 3DFlex half map B

Fileemd_64481_half_map_1.map
Annotation3DFlex half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3DFlex half map A

Fileemd_64481_half_map_2.map
Annotation3DFlex half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helicase-primase complex from human herpesvirus 1

EntireName: Helicase-primase complex from human herpesvirus 1
Components
  • Complex: Helicase-primase complex from human herpesvirus 1
    • Complex: helicase
      • Protein or peptide: DNA replication helicase
    • Complex: primase
      • Protein or peptide: Ubiquitin-like protein SMT3,DNA primase
      • Protein or peptide: Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein
    • Complex: ssDNA
      • DNA: synthetic DNA
  • Ligand: Pritelivir
  • Ligand: ZINC ION

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Supramolecule #1: Helicase-primase complex from human herpesvirus 1

SupramoleculeName: Helicase-primase complex from human herpesvirus 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: helicase

SupramoleculeName: helicase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)

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Supramolecule #3: primase

SupramoleculeName: primase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)

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Supramolecule #4: ssDNA

SupramoleculeName: ssDNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4

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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 (Herpes simplex virus type 1)
Molecular weightTheoretical: 104.354164 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYYGAWSHP QFEKGGGSGG GSGGSAWSHP QFEKGAHHHH HHGSLEVLFQ GPMAAAGGER QLDGQKPGPP HLQQPGDRPA VPGRAEAFL NFTSMHGVQP ILKRIRELSQ QQLDGAQVPH LQWFRDVAAL ESPAGLPLRE FPFAVYLITG NAGSGKSTCV Q TINEVLDC ...String:
MSYYGAWSHP QFEKGGGSGG GSGGSAWSHP QFEKGAHHHH HHGSLEVLFQ GPMAAAGGER QLDGQKPGPP HLQQPGDRPA VPGRAEAFL NFTSMHGVQP ILKRIRELSQ QQLDGAQVPH LQWFRDVAAL ESPAGLPLRE FPFAVYLITG NAGSGKSTCV Q TINEVLDC VVTGATRIAA QNMYAKLSGA FLSRPINTIF HEFGFRGNHV QAQLGQYPYT LTSNPASLED LQRRDLTYYW EV ILDLTKR ALAASGGEEL RNEFRALAAL ERTLGLAEGA LTRLAPATHG ALPAFTRSNV IVIDEAGLLG RHLLTAVVYC WWM INALYH TPQYAARLRP VLVCVGSPTQ TASLESTFEH QKLRCSVRQS ENVLTYLICN RTLREYARLS YSWAIFINNK RCVE HEFGN LMKVLEYGLP ITEEHMQFVD RFVVPENYIT NPANLPGWTR LFSSHKEVSA YMAKLHAYLK VTREGEFVVF TLPVL TFVS VKEFDEYRRL THQPGLTIEK WLTANASRIT NYSQSQDQDA GHMRCEVHSK QQLVVARNDV TYVLNSQIAV TARLRK LVF GFSGTFRAFE AVLRDDSFVK TQGETSVEFA YRFLSRLIFS GLISFYNFLQ RPGLDATQRT LAYARMGELT AEILSLR PK SSGVPTQASV MADAGAPGER AFDFKQLGPR DGGPDDFPDD DLDVIFAGLD EQQLDVFYCH YTPGEPETTA AVHTQFAL L KRAFLGRFRI LQELFGEAFE VAPFSTYVDN VIFRGCEMLT GSPRGGLMSV ALQTDNYTLM GYTYARVFAF ADELRRRHA TANVAELLEE APLPYVVLRD QHGFMSVVNT NISEFVESID STELAMAINA DYGISSKLAM TITRSQGLSL DKVAICFTPG NLRLNSAYV AMSRTTSSEF LRMNLNPLRE RHERDDVISE HILSALRDPN VVIVY

UniProtKB: DNA replication helicase

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Macromolecule #2: Ubiquitin-like protein SMT3,DNA primase

MacromoleculeName: Ubiquitin-like protein SMT3,DNA primase / type: protein_or_peptide / ID: 2 / Details: SUMOstar / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 130.398977 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGITSLYK KAGFLQLGSL QDSEVNQEAK PEVKPEVKPE THINLKVSDG SSEIFFKIKK TTPLRRLME AFAKRQGKEM DSLTFLYDGI EIQADQTPED LDMEDNDIIE AHREQIGGMG QEDGNRGERR AAGTPVEVTA L YATDGCVI ...String:
MSYYHHHHHH DYDIPTTENL YFQGITSLYK KAGFLQLGSL QDSEVNQEAK PEVKPEVKPE THINLKVSDG SSEIFFKIKK TTPLRRLME AFAKRQGKEM DSLTFLYDGI EIQADQTPED LDMEDNDIIE AHREQIGGMG QEDGNRGERR AAGTPVEVTA L YATDGCVI TSSIALLTNS LLGAEPVYIF SYDAYTHDGR ADGPTEQDRF EESRALYQAS GGLNGDSFRV TFCLLGTEVG GT HQARGRT RPMFVCRFER ADDVAALQDA LAHGTPLQPD HIAATLDAEA TFALHANMIL ALTVAINNAS PRTGRDAAAA QYD QGASLR SLVGRTSLGQ RGLTTLYVHH EVRVLAAYRR AYYGSAQSPF WFLSKFGPDE KSLVLTTRYY LLQAQRLGGA GATY DLQAI KDICATYAIP HAPRPDTVSA ASLTSFAAIT RFCCTSQYAR GAAAAGFPLY VERRIAADVR ETSALEKFIT HDRSC LRVS DREFITYIYL AHFECFSPPR LATHLRAVTT HDPNPAASTE QPSPLGREAV EQFFCHVRAQ LNIGEYVKHN VTPRET VLD GDTAKAYLRA RTYAPGALTP APAYCGAVDS ATKMMGRLAD AEKLLVPRGW PAFAPASPGE DTAGGTPPPQ TCGIVKR LL RLAATEQQGP TPPAIAALIR NAAVQTPLPV YRISMVPTGQ AFAALAWDDW ARITRDARLA EAVVSAEAAA HPDHGALG R RLTDRIRAQG PVMPPGGLDA GGQMYVNRNE IFNGALAITN IILDLDIALK EPVPFRRLHE ALGHFRRGAL AAVQLLFPA ARVDPDAYPC YFFKSACRPG PASVGSGSGL GNDDDGDWFP CYDDAGDEEW AEDPGAMDTS HDPPDDEVAY FDLCHEVGPT AEPRETDSP VCSCTDKIGL RVCMPVPAPY VVHGSLTMRG VARVIQQAVL LDRDFVEAIG SYVKNFLLID TGVYAHGHSL R LPYFAKIA PDGPACGRLL PVFVIPPACK DVPAFVAAHA DPRRFHFHAP PTYLASPREI RVLHSLGGDY VSFFERKASR NA LEHFGRR ETLTEVLGRY NVQPDAGGTV EGFASELLGR IVACIETHFP EHAGEYQAVS VRRAVSKDDW VLLQLVPVRG TLQ QSLSCL RFKHGRASRA TARTFVALSV GANNRLCVSL CQQCFAAKCD SNRLHTLFTI DAGTPCSPSV PCSTSQPSS

UniProtKB: Small ubiquitin-related modifier, DNA primase

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Macromolecule #3: Ubiquitin-like protein SMT3,DNA helicase/primase complex-associat...

MacromoleculeName: Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein
type: protein_or_peptide / ID: 3 / Details: SUMOstar / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 95.846422 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGITSLYK KAGFLQLGSL QDSEVNQEAK PEVKPEVKPE THINLKVSDG SSEIFFKIKK TTPLRRLME AFAKRQGKEM DSLTFLYDGI EIQADQTPED LDMEDNDIIE AHREQIGGMD TADIVWVEES VSAITLYAVW L PPRAREYF ...String:
MSYYHHHHHH DYDIPTTENL YFQGITSLYK KAGFLQLGSL QDSEVNQEAK PEVKPEVKPE THINLKVSDG SSEIFFKIKK TTPLRRLME AFAKRQGKEM DSLTFLYDGI EIQADQTPED LDMEDNDIIE AHREQIGGMD TADIVWVEES VSAITLYAVW L PPRAREYF HALVYFVCRN AAGEGRARFA EVSVTATELR DFYGSADVSV QAVVAAARAA TTPAASPLEP LENPTLWRAL YA CVLAALE RQTGPVALFA PLRIGSDPRT GLVVKVERAS WGPPAAPRAA LLVAEANIDI DPMALAARVA EHPDARLAWA RLA AIRDTP QCASAASLTV NITTGTALFA REYQTLAFPP IKKEGAFGDL VEVCEVGLRP RGHPQRVTAR VLLPRDYDYF VSAG EKFSA PALVALFRQW HTTVHAAPGA LAPVFAFLGP EFEVRGGPVP YFAVLGFPGW PTFTVPATAE SARDLVRGAA AAYAA LLGA WPAVGARVVL PPRAWPGVAS AAAGCLLPAV REAVARWHPA TKIIQLLDPP AAVGPVWTAR FCFPGLRAQL LAALAD LGG SGLADPHGRT GLARLDALVV AAPSEPWAGA VLERLVPDTC NACPALRQLL GGVMAAVCLQ IEETASSVKF AVCGGDG GA FWGVFNVDPQ DADAASGVIE DARRAIETAV GAVLRANAVR LRHPLCLALE GVYTHAVAWS QAGVWFWNSR DNTDHLGG F PLRGPAYTTA AGVVRDTLRR VLGLTTACVP EEDALTARGL MEDACDRLIL DAFNKRLDAE YWSVRVSPFE ASDPLPPTA FRGGALLDAE HYWRRVVRVC PGGGESVGVP VDLYPRPLVL PPVDCAHHLR EILREIELVF TGVLAGVWGE GGKFVYPFDD KMSFLFA

UniProtKB: Small ubiquitin-related modifier, DNA helicase/primase complex-associated protein

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Macromolecule #4: synthetic DNA

MacromoleculeName: synthetic DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.780199 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #5: Pritelivir

MacromoleculeName: Pritelivir / type: ligand / ID: 5 / Number of copies: 1 / Formula: A1BXB
Molecular weightTheoretical: 402.491 Da

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 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: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: 3D-Flex refinement / Number images used: 99000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER

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