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- EMDB-49269: The rigid portion of Cryo-EM structure of Herpesvirus Helicase-Pr... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49269
TitleThe rigid portion of Cryo-EM structure of Herpesvirus Helicase-Primase complex with amenamevir
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 helicase/primase complex-associated protein
KeywordsInhibitor / Helicase / Primase / Herpesvirus / REPLICATION / TRANSFERASE
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA-directed RNA polymerase activity / DNA replication / host cell nucleus / zinc ion binding
Similarity search - Function
DNA helicase/primase complex-associated protein / Herpesvirus DNA helicase/primase complex associated protein / DNA primase / Herpesviridae UL52/UL70 DNA primase
Similarity search - Domain/homology
DNA helicase/primase complex-associated protein / DNA primase
Similarity search - Component
Biological speciesHerpesviridae (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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 17, 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_49269.png

Downloads & links

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Map

FileDownload / File: emd_49269.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: 0.113
Minimum - Maximum-0.0017999762 - 2.4345043
Average (Standard dev.)0.00066832657 (±0.020296222)
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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Half map: #1

Fileemd_49269_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49269_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 helicase/primase complex-associated protein

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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: 114.427352 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GQEDGNRGER RAAGTPVEVT ALYATDGCVI TSSIALLTNS LLGAEPVYIF SYDAYTHDGR ADGPTEQDRF EESRALYQAS GGLNGDSFR VTFCLLGTEV GGTHQARGRT RPMFVCRFER ADDVAALQDA LAHGTPLQPD HIAATLDAEA TFALHANMIL A LTVAINNA ...String:
GQEDGNRGER RAAGTPVEVT ALYATDGCVI TSSIALLTNS LLGAEPVYIF SYDAYTHDGR ADGPTEQDRF EESRALYQAS GGLNGDSFR VTFCLLGTEV GGTHQARGRT RPMFVCRFER ADDVAALQDA LAHGTPLQPD HIAATLDAEA TFALHANMIL A LTVAINNA SPRTGRDAAA AQYDQGASLR SLVGRTSLGQ RGLTTLYVHH EVRVLAAYRR AYYGSAQSPF WFLSKFGPDE KS LVLTTRY YLLQAQRLGG AGATYDLQAI KDICATYAIP HAPRPDTVSA ASLTSFAAIT RFCCTSQYAR GAAAAGFPLY VER RIAADV RETSALEKFI THDRSCLRVS DREFITYIYL AHFECFSPPR LATHLRAVTT HDPNPAASTE QPSPLGREAV EQFF CHVRA QLNIGEYVKH NVTPRETVLD GDTAKAYLRA RTYAPGALTP APAYCGAVDS ATKMMGRLAD AEKLLVPRGW PAFAP ASPG EDTAGGTPPP QTCGIVKRLL RLAATEQQGP TPPAIAALIR NAAVQTPLPV YRISMVPTGQ AFAALAWDDW ARITRD ARL AEAVVSAEAA AHPDHGALGR RLTDRIRAQG PVMPPGGLDA GGQMYVNRNE IFNGALAITN IILDLDIALK EPVPFRR LH EALGHFRRGA LAAVQLLFPA ARVDPDAYPC YFFKSACRPG PASVGSGSGL GNDDDGDWFP CYDDAGDEEW AEDPGAMD T SHDPPDDEVA YFDLCHEVGP TAEPRETDSP VCSCTDKIGL RVCMPVPAPY VVHGSLTMRG VARVIQQAVL LDRDFVEAI GSYVKNFLLI DTGVYAHGHS LRLPYFAKIA PDGPACGRLL PVFVIPPACK DVPAFVAAHA DPRRFHFHAP PTYLASPREI RVLHSLGGD YVSFFERKAS RNALEHFGRR ETLTEVLGRY NVQPDAGGTV EGFASELLGR IVACIETHFP EHAGEYQAVS V RRAVSKDD WVLLQLVPVR GTLQQSLSCL RFKHGRASRA TARTFVALSV GANNRLCVSL CQQCFAAKCD SNRLHTLFTI DA GTPCSPS VPCSTSQPSS

UniProtKB: DNA primase

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Macromolecule #2: DNA helicase/primase complex-associated protein

MacromoleculeName: DNA helicase/primase complex-associated protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Herpesviridae (virus)
Molecular weightTheoretical: 79.704336 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDTADIVWVE ESVSAITLYA VWLPPAREYF HALVYFVCRN AAGEGRARFA EVSVTATELR DFYGSADVSV QAVVAAARAA TTPAASPLE PLENPTLWRA LYACVLAALE RQTGPVALFA PLRIGSDPRT GLVVKVERAW GPPAAPRAAL LVAEANIDID P MALAARVA ...String:
MDTADIVWVE ESVSAITLYA VWLPPAREYF HALVYFVCRN AAGEGRARFA EVSVTATELR DFYGSADVSV QAVVAAARAA TTPAASPLE PLENPTLWRA LYACVLAALE RQTGPVALFA PLRIGSDPRT GLVVKVERAW GPPAAPRAAL LVAEANIDID P MALAARVA EHPDARLAWA RLAAIRDTPQ CASAASLTVN ITTGTALFAR EYQTLAFPPI KKEGAFGDLV EVCEVGLRPR GH PQRVTAR VLLPRDYDYF VSAGEKFSAP ALVALFRQWH TTVHAAPALA PVFAFLGPEF EVRGGPVPYF AVLGFPGWPT FTV PATAES ARDLVRGAAA AYAALLGAWP AVGARVVLPP RAWPGVASAA AGCLLPAVRE AVARWHPATK IIQLLDPPAA VGPV WTARF CFPGLRAQLL AALADLGGSG LADPHGRTGL ARLDALVVAA PSEPWAGAVL ERLVPDTCNA CPALRQLLGG VMAAV CLQI EETASSVKFA VCGGDGGAFW GVFNVDPQDA DAASGVIEDA RRAIETAVGA VLRANAVRLR HPLCLALEGV YTHAVA WSQ AGVWFWNSRD NTDHLGGFPL RGPAYTTAAG VVRDTLRRVL GLTTACVPEE DALTARGLME DACDRLILDA FNKRLDA EY WSVRVSPFEA SDPLPPTAFR GGALLDAEHY WRRVVRVCPG GGESVGVPVD LYPRPLVLPP VDCAHHLREI LREIELVF T GVLAGVWGEG GKFVYPFDDK MSFLFA

UniProtKB: DNA helicase/primase complex-associated protein

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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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115543
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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