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- EMDB-49326: The flexible portion of Cryo-EM structure of Herpesvirus Helicase... -

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Basic information

Entry
Database: EMDB / ID: EMD-49326
TitleThe flexible portion of Cryo-EM structure of Herpesvirus Helicase-Primase complex with amenamevir
Map data
Sample
  • Complex: The ternary complex of HSV-1 UL8/UL52/UL5 helicase-primase complex
    • Protein or peptide: DNA primase
    • Protein or peptide: DNA replication helicase
  • Ligand: Amenamevir
KeywordsInhibitor / Herpesvirus / Helicase / Primase / Pritelivir / REPLICATION / TRANSFERASE-INHIBITOR 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 replication helicase, Herpesvirus / Helicase / DNA primase / Herpesviridae UL52/UL70 DNA primase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA replication helicase / DNA primase
Similarity search - Component
Biological speciesHerpesviridae (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYao Q / Yu X / Baker D / Jensen G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure and Inhibition Mechanism of Herpesvirus Helicase-Primase
Authors: Yao Q / Mercier A
History
DepositionFeb 19, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49326.png

Downloads & links

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Map

FileDownload / File: emd_49326.map.gz / Format: CCP4 / Size: 282.6 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 420 pix.
= 306.18 Å		0.73 Å/pix.
x 420 pix.
= 306.18 Å		0.73 Å/pix.
x 420 pix.
= 306.18 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.154
Minimum - Maximum-0.0017781525 - 2.5370674
Average (Standard dev.)0.0006510259 (±0.01998212)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 306.18 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49326_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49326_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49326_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The ternary complex of HSV-1 UL8/UL52/UL5 helicase-primase complex

EntireName: The ternary complex of HSV-1 UL8/UL52/UL5 helicase-primase complex
Components
  • Complex: The ternary complex of HSV-1 UL8/UL52/UL5 helicase-primase complex
    • Protein or peptide: DNA primase
    • Protein or peptide: DNA replication helicase
  • Ligand: Amenamevir

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Supramolecule #1: The ternary complex of HSV-1 UL8/UL52/UL5 helicase-primase complex

SupramoleculeName: The ternary complex of HSV-1 UL8/UL52/UL5 helicase-primase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Herpesviridae (virus)

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Macromolecule #1: DNA primase

MacromoleculeName: DNA primase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Source (natural)Organism: Herpesviridae (virus)
Molecular weightTheoretical: 114.602625 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 GATATYDLQA 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 #2: DNA replication helicase

MacromoleculeName: DNA replication helicase / type: protein_or_peptide / ID: 2 / 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: Herpesviridae (virus)
Molecular weightTheoretical: 94.753688 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TSMHGVQPIL KRIRELSQQQ LDGAQVPHLQ WFRDVAALES PAGLPLREFP FAVYLITGNA GSGKSTCVQT INEVLDCVVT GATRIAAQN MYAKLSGAFL SRPINTIFHE FGFRGNHVQA QLGQYPYTLT SNPASLEDLQ RRDLTYYWEV ILDLTKRALA A SGGEELRN ...String:
TSMHGVQPIL KRIRELSQQQ LDGAQVPHLQ WFRDVAALES PAGLPLREFP FAVYLITGNA GSGKSTCVQT INEVLDCVVT GATRIAAQN MYAKLSGAFL SRPINTIFHE FGFRGNHVQA QLGQYPYTLT SNPASLEDLQ RRDLTYYWEV ILDLTKRALA A SGGEELRN EFRALAALER TLGLAEGALT RLAPATHGAL PAFTRSNVIV IDEAGLLGRH LLTAVVYCWW MINALYHTPQ YA ARLRPVL VCVGSPTQTA SLESTFEHQK LRCSVRQSEN VLTYLICNRT LREYARLSYS WAIFINNKRC VEHEFGNLMK VLE YGLPIT EEHMQFVDRF VVPENYITNP ANLPGWTRLF SSHKEVSAYM AKLHAYLKVT REGEFVVFTL PVLTFVSVKE FDEY RRLTH QPGLTIEKWL TANASRITNY SQSQDQDAGH MRCEVHSKQQ LVVARNDVTY VLNSQIAVTA RLRKLVFGFS GTFRA FEAV LRDDSFVKTQ GETSVEFAYR FLSRLIFSGL ISFYNFLQRP GLDATQRTLA YARMGELTAE ILSLRPKSSG VPTQAS VMA DAGAPGERAF DFKQLGPRDG GPDDFPDDDL DVIFAGLDEQ QLDVFYCHYT PGEPETTAAV HTQFALLKRA FLGRFRI LQ ELFGEAFEVA PFSTYVDNVI FRGCEMLTGS PRGGLMSVAL QTDNYTLMGY TYARVFAFAD ELRRRHATAN VAELLEEA P LPYVVLRDQH GFMSVVNTNI SEFVESIDST ELAMAINADY GISSKLAMTI TRSQGLSLDK VAICFTPGNL RLNSAYVAM SRTTSSEFLR MNLNPLRERH ERDDVISEHI LSALRDPNVV IVY

UniProtKB: DNA replication helicase

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Macromolecule #3: Amenamevir

MacromoleculeName: Amenamevir / type: ligand / ID: 3 / 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

Concentration1.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Detector mode: COUNTING / 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: 2.2 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 115543
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.11)
FSC plot (resolution estimation)

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