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- EMDB-49291: The flexible portion of Cryo-EM structure of Herpesvirus Helicase... -

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Basic information

Entry
Database: EMDB / ID: EMD-49291
TitleThe flexible portion of Cryo-EM structure of Herpesvirus Helicase-Primase complex prepared with forked DNA, ATP-gamma-S and Pritelivir
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: Pritelivir
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: 3.4 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_49291.png

Downloads & links

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Map

FileDownload / File: emd_49291.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-0.0017719486 - 1.960684
Average (Standard dev.)0.00072665355 (±0.019371372)
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_49291_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49291_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_49291_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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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: Pritelivir

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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: 111.224039 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: PVEVTALYAT DGCVITSSIA LLTNSLLGAE PVYIFSYDAY THTGRADGPT EQDRFEESRA LYQASGGLNG DSFRVTFCLL GTEVGGTHQ ARGRTRPMFV CRFERADDVA ALQDALAHGT PLQPDHIAAT LDAEATFALH ANMILALTVA INNASPRTGR D AAAAQYDQ ...String:
PVEVTALYAT DGCVITSSIA LLTNSLLGAE PVYIFSYDAY THTGRADGPT EQDRFEESRA LYQASGGLNG DSFRVTFCLL GTEVGGTHQ ARGRTRPMFV CRFERADDVA ALQDALAHGT PLQPDHIAAT LDAEATFALH ANMILALTVA INNASPRTGR D AAAAQYDQ GASLRSLVGR TSLGQRGLTT LYVHHEVRVL AAYRRAYYGS AQSPFWFLSK FGPDEKSLVL TTRYYLLQAQ RL GGATATY 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 LGGDYVSFFE RKASRNALE HFGRRETLTE VLGRYNVQPD AGGTVEGFAS ELLGRIVACI ETHFPEHAGE YQAVSVRRAV SKDDWVLLQL V PVRGTLQQ SLSCLRFKHG RASRATARTF VALSVGANNR LCVSLCQQCF AAKCDSNRLH TLFTID

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: 95.275297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: FLNFTSMHGV QPILKRIREL SQQQLDGAQV PHLQWFRDVA ALESPAGLPL REFPFAVYLI TGNAGSGKST CVQTINEVLD CVVTGATRI AAQNMYAKLS GAFLSRPINT IFHEFGFRGN HVQAQLGQYP YTLTSNPASL EDLQRRDLTY YWEVILDLTK R ALAASGGE ...String:
FLNFTSMHGV QPILKRIREL SQQQLDGAQV PHLQWFRDVA ALESPAGLPL REFPFAVYLI TGNAGSGKST CVQTINEVLD CVVTGATRI AAQNMYAKLS GAFLSRPINT IFHEFGFRGN HVQAQLGQYP YTLTSNPASL EDLQRRDLTY YWEVILDLTK R ALAASGGE ELRNEFRALA ALERTLGLAE GALTRLAPAT HGALPAFTRS NVIVIDEAGL LGRHLLTAVV YCWWMINALY HT PQYAARL RPVLVCVGSP TQTASLESTF EHQKLRCSVR QSENVLTYLI CNRTLREYAR LSYSWAIFIN NKRCVEHEFG NLM KVLEYG LPITEEHMQF VDRFVVPENY ITNPANLPGW TRLFSSHKEV SAYMAKLHAY LKVTREGEFV VFTLPVLTFV SVKE FDEYR RLTHQPGLTI EKWLTANASR ITNYSQSQDQ DAGHMRCEVH SKQQLVVARN DVTYVLNSQI AVTARLRKLV FGFSG TFRA FEAVLRDDSF VKTQGETSVE FAYRFLSRLI FSGLISFYNF LQRPGLDATQ RTLAYARMGE LTAEILSLRP KSSGVP TQA SVMADAGAPG ERAFDFKQLG PRDGGPDDFP DDDLDVIFAG LDEQQLDVFY CHYTPGEPET TAAVHTQFAL LKRAFLG RF RILQELFGEA FEVAPFSTYV DNVIFRGCEM LTGSPRGGLM SVALQTDNYT LMGYTYARVF AFADELRRRH ATANVAEL L EEAPLPYVVL RDQHGFMSVV NTNISEFVES IDSTELAMAI NADYGISSKL AMTITRSQGL SLDKVAICFT PGNLRLNSA YVAMSRTTSS EFLRMNLNPL RERHERDDVI SEHILSALRD PNVVIVY

UniProtKB: DNA replication helicase

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Macromolecule #3: Pritelivir

MacromoleculeName: Pritelivir / type: ligand / ID: 3 / Number of copies: 1 / Formula: A1BXB
Molecular weightTheoretical: 402.491 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 / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III

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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: 100.0 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 155321
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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