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- EMDB-49277: The flexible portion of Cryo-EM structure of Herpesvirus Helicase... -

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Basic information

Entry
Database: EMDB / ID: EMD-49277
TitleThe flexible portion of Cryo-EM structure of Herpesvirus Helicase-Primase complex prepared with forked DNA and ATP-gamma-S
Map data
Sample
  • Complex: The ternary complex of HSV-1 helicase-primase complex of UL8/UL52/UL5
    • Protein or peptide: DNA primase
    • Protein or peptide: DNA replication helicase
KeywordsHelicase / Primase / Forked DNA / REPLICATION / TRANSFERASE
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: 3.8 Å
AuthorsYao Q / Yu X
Funding support United States, 1 items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: To Be Published
Title: Structure and Inhibition Mechanism of Herpesvirus Helicase-Primase
Authors: Yao Q / Mercier A
History
DepositionFeb 18, 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_49277.png

Downloads & links

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Map

FileDownload / File: emd_49277.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: 0.145
Minimum - Maximum-0.001814243 - 2.0934334
Average (Standard dev.)0.0004615276 (±0.016229216)
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_49277_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49277_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49277_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 helicase-primase complex of UL8/UL52/UL5

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

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

SupramoleculeName: The ternary complex of HSV-1 helicase-primase complex of UL8/UL52/UL5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 94.733156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: PVEVTALYAT DGCVITSSIA LLTNSLLGAE PVYIFSYDAY THDGRADGPT EQDRFEESRA LYQASGGLNG DSFRVTFCLL GTEVGGTHQ ARGRTRPMFV CRFERADDVA ALQDALAHGT PLQPDHIAAT LDAEATFALH ANMILALTVA INNASPRTGR D AAAAQYDQ ...String:
PVEVTALYAT DGCVITSSIA LLTNSLLGAE PVYIFSYDAY THDGRADGPT EQDRFEESRA LYQASGGLNG DSFRVTFCLL GTEVGGTHQ ARGRTRPMFV CRFERADDVA ALQDALAHGT PLQPDHIAAT LDAEATFALH ANMILALTVA INNASPRTGR D AAAAQYDQ GASLRSLVGR TSLGQRGLTT LYVHHEVRVL AAYRRAYYGS AQSPFWFLSK FGPDEKSLVL TTRYYLLQAQ RL GGAGATY DLQAIKDICA TYAIPHAPRP DTVSAASLTS FAAITRFCCT SQYARGAAAA GFPLYVERRI AADVRETSAL EKF ITHDRS CLRVSDREFI TYIYLAHFEC FSPPRLATHL RAVTTHDPNP AASTEQPSPL GREAVEQFFC HVRAQLNIGE YVKH NVTPR ETVLDGDTAK AYLRARTYAP GALTPAPAYC GAVDSATKMM GRLADAEKLL VPRGWPAFAP ASPGEDTAGG TPPPQ TCGI VKRLLRLAAT EQQGPTPPAI AALIRNAAVQ TPLPVYRISM VPTGQAFAAL AWDDWARITR DARLAEAVVS AEAAAH PDH GALGRRLTDR IRAQGPVMPP GGLDAGGQMY VNRNEIFNGA LAITNIILDL DIALKEPVPF RRLHEALGHF RRGALAA VQ LLFPAARVDP DAYPCYFFKS ACRPGPASVG SGSGLGNDDD GDWFPCYDDA GDEEWAEDPG AMDTSHDPPD DEVAYFDL C HEVGPTAEPR ETDSPVCSCT DKIGLRVCMP VPAPYVVHGS LTMRGVARVI QQAVLLDRDF VEAIGSYVKN FLLIDTGVY AHGHSLRLPY FAKIAPDGPA CGRLLPVFVI PPACKDVPAF VAAHADPRRF HFHAPPTYLA SPREIRVLHS LGGDYV

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: 95.014969 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NFTSMHGVQP ILKRIRELSQ QQLDGAQVPH LQWFRDVAAL ESPAGLPLRE FPFAVYLITG NAGSGKSTCV QTINEVLDCV VTGATRIAA QNMYAKLSGA FLSRPINTIF HEFGFRGNHV QAQLGQYPYT LTSNPASLED LQRRDLTYYW EVILDLTKRA L AASGGEEL ...String:
NFTSMHGVQP ILKRIRELSQ QQLDGAQVPH LQWFRDVAAL ESPAGLPLRE FPFAVYLITG NAGSGKSTCV QTINEVLDCV VTGATRIAA QNMYAKLSGA FLSRPINTIF HEFGFRGNHV QAQLGQYPYT LTSNPASLED LQRRDLTYYW EVILDLTKRA L AASGGEEL RNEFRALAAL ERTLGLAEGA LTRLAPATHG ALPAFTRSNV IVIDEAGLLG RHLLTAVVYC WWMINALYHT PQ YAARLRP VLVCVGSPTQ TASLESTFEH QKLRCSVRQS ENVLTYLICN RTLREYARLS YSWAIFINNK RCVEHEFGNL MKV LEYGLP ITEEHMQFVD RFVVPENYIT NPANLPGWTR LFSSHKEVSA YMAKLHAYLK VTREGEFVVF TLPVLTFVSV KEFD EYRRL THQPGLTIEK WLTANASRIT NYSQSQDQDA GHMRCEVHSK QQLVVARNDV TYVLNSQIAV TARLRKLVFG FSGTF RAFE AVLRDDSFVK TQGETSVEFA YRFLSRLIFS GLISFYNFLQ RPGLDATQRT LAYARMGELT AEILSLRPKS SGVPTQ ASV MADAGAPGER AFDFKQLGPR DGGPDDFPDD DLDVIFAGLD EQQLDVFYCH YTPGEPETTA AVHTQFALLK RAFLGRF RI LQELFGEAFE VAPFSTYVDN VIFRGCEMLT GSPRGGLMSV ALQTDNYTLM GYTYARVFAF ADELRRRHAT ANVAELLE E APLPYVVLRD QHGFMSVVNT NISEFVESID STELAMAINA DYGISSKLAM TITRSQGLSL DKVAICFTPG NLRLNSAYV AMSRTTSSEF LRMNLNPLRE RHERDDVISE HILSALRDPN VVIVY

UniProtKB: DNA replication helicase

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 5.84 sec. / 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
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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52547
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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