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- EMDB-49749: Cryo-EM structure of UL5/UL8/UL52 in the presence of ATPgS -

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Basic information

Entry
Database: EMDB / ID: EMD-49749
TitleCryo-EM structure of UL5/UL8/UL52 in the presence of ATPgS
Map data
Sample
  • Complex: UL5/UL8/UL52
    • Protein or peptide: UL8
    • Protein or peptide: UL52
    • Protein or peptide: UL5
KeywordsPrimase / Helicase / DNA replication / VIRAL PROTEIN
Biological speciesHuman alphaherpesvirus 1 (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBermek O / Krahn JM / Viverette EG / Peele W / Dandey VP / Borgnia MJ / Williams RS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: To Be Published
Title: Molecular Architecture and Antiviral Inhibition of Helicase/Primase Complex of Herpes Simplex Virus-1
Authors: Bermek O / Krahn JM / Viverette EG / Peele W / Dandey VP / Borgnia MJ / Williams RS
History
DepositionMar 17, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49749.png

Downloads & links

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Map

FileDownload / File: emd_49749.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.29 Å/pix.
x 240 pix.
= 310.344 Å		1.29 Å/pix.
x 240 pix.
= 310.344 Å		1.29 Å/pix.
x 240 pix.
= 310.344 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2931 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-46.021909999999998 - 65.554419999999993
Average (Standard dev.)0.000000000010086 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 310.344 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49749_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_49749_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 : UL5/UL8/UL52

EntireName: UL5/UL8/UL52
Components
  • Complex: UL5/UL8/UL52
    • Protein or peptide: UL8
    • Protein or peptide: UL52
    • Protein or peptide: UL5

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Supramolecule #1: UL5/UL8/UL52

SupramoleculeName: UL5/UL8/UL52 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: UL8

MacromoleculeName: UL8 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRGSHHHHHH GMENLYFQ M DTADIVWVEE SVSAITLYAV WLPPRAREYF HALVYFVCRN AAGEGRARFA EVSVTATELR DFYGSADVSV QAVVAAARAA TTPAASPLEP LENPTLWRAL YACVLAALER QTGPVALFAP LRIGSDPRTG LVVKVERASW GPPAAPRAAL ...String:
MRGSHHHHHH GMENLYFQ M DTADIVWVEE SVSAITLYAV WLPPRAREYF HALVYFVCRN AAGEGRARFA EVSVTATELR DFYGSADVSV QAVVAAARAA TTPAASPLEP LENPTLWRAL YACVLAALER QTGPVALFAP LRIGSDPRTG LVVKVERASW GPPAAPRAAL LVAEANIDID PMALAARVAE HPDARLAWAR LAAIRDTPQC ASAASLTVNI TTGTALFARE YQTLAFPPIK KEGAFGDLVE VCEVGLRPRG HPQRVTARVL LPRDYDYFVS AGEKFSAPAL VALFRQWHTT VHAAPGALAP VFAFLGPEFE VRGGPVPYFA VLGFPGWPTF TVPATAESAR DLVRGAAAAY AALLGAWPAV GARVVLPPRA WPGVASAAAG CLLPAVREAV ARWHPATKII QLLDPPAAVG PVWTARFCFP GLRAQLLAAL ADLGGSGLAD PHGRTGLARL DALVVAAPSE PWAGAVLERL VPDTCDACPA LRQLLGGVMA AVCLQIEETA SSVKFAVCGG DGGAFWGVFN VDPQDADAAS GVIEDARRAI ETAVGAVLRA NGLRLRHPLC LALEGVYTHA VAWNQAGVWF WNSRDNTDHL GGFPLRGPAY TTAAGVVRDT LRRVLGLTTA GVPEEDALTA RGLMEDACDR LIVDAFNKRL DAEYWSVRVS PFEASDPLPP TAFRGGALLD AEHYWRRVVR VCPGGGESVG VPVDLYPRPL VLPPVDCAHH LREILREIEL VFTGVLAGVW GEGGKFVYPF DDKMSFLFA

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Macromolecule #2: UL52

MacromoleculeName: UL52 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGQEDGNRGE RRAAGTPVEV TALYATDGCV ITSSIALLTN SLLGAEPVYI FSYDAYTHDG RADGPTEQDR FEESRALYQA SGGLNGDSFR VTFCLLGTEV GGTHQARGRT RPMFVCRFER ADDVAALQEA LAHGTPLQPD HIAATLDAEA TFALHANMIL ALTVAVNNAS ...String:
MGQEDGNRGE RRAAGTPVEV TALYATDGCV ITSSIALLTN SLLGAEPVYI FSYDAYTHDG RADGPTEQDR FEESRALYQA SGGLNGDSFR VTFCLLGTEV GGTHQARGRT RPMFVCRFER ADDVAALQEA LAHGTPLQPD HIAATLDAEA TFALHANMIL ALTVAVNNAS PRTGRDAAAA QYDQGASLRS LVGRTSLGQR GLTTLYVHHE ARVLAAYRRA YYGSAQSPFW FLSKFGPDEK SLVLTTRYYL LQAQRLGGAG ATYDLQAIKD ICATYAIPHA PRPDTVSAAS LTSFAAITRF CCTSQYARGA AAAGFPLYVE RRIAADVRET SALEKFITHD RSCLRVSDRE FITYIYLAHF ECFSPPRLAT HLRAVTTHDP NPAASTEQPS PLGREAVEQF FCHVRAQLNI GEYVKHNVTP RETVLDGDTA KAYLRARTYA PGALTPAPAY CGAVDSATKM MGRLADAEKL LVPRGWPAFA PASPGEDTAG GTPPPQTCGI VKRLLRLAAT EQQDTTPPAI AALIRNAAVQ TPLPVYRISM VPTGQAFAAL AWDDWARITR DARLAEAVVS AEAAAHPDHG ALGRRLTDRI RAQGPVMPPG GLDAGGQMYV NRNEIFNGAL AITNIILDLD IALKEPVPFR RLHEALGHFR RGALAAVQLL FPAARVDPDA YPCYFFKSAC RPGPASVGSG SGLGNDDDGD WFPCYDDAGD EEWAEDPGAM DTSHDPPDDE VAYFDLCHEV GPTAEPRETD SPVCSCTDKI GLRVCMPVPA PYVVHGSLTM RGVARVIQQA VLLDRDFVEA IGSYVKNFLL IDTGVYAHGH SLRLPYFAKI APDGPACGRL LPVFVIPPAC KDVPAFVAAH ADPRRFHFHA PPTYLASPRE IRVLHSLGGD YVSFFERKAS RNALEHFGRR ETLTEVLGRY NVQPDAGGTV EGFASELLGR IVACIETHFP EHAGEYQAVS VRRAVSKDDW VLLQLVPVRG TLQQSLSCLR FKHGRASRAT ARTFVALSVG ANNRLCVSLC QQCFAAKCDS NRLHTLFTID AGTPCSPSVP CSTSQPSS

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Macromolecule #3: UL5

MacromoleculeName: UL5 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAAGGERQL DGQKPGPPHL QQPGDRPAVP GRAEAFLNFT SMHGVQPILK RIRELSQQQL DGAQVPRLQW FRDVAALESP AGLPLREFPF AVYLITGNAG SGKSTCVQTI NEVLDCVVTG ATRIAAQNMY AKLSGAFLSR PINTIFHEFG FRGNHVQAQL GQYPYTLTSN ...String:
MAAAGGERQL DGQKPGPPHL QQPGDRPAVP GRAEAFLNFT SMHGVQPILK RIRELSQQQL DGAQVPRLQW FRDVAALESP AGLPLREFPF AVYLITGNAG SGKSTCVQTI NEVLDCVVTG ATRIAAQNMY AKLSGAFLSR PINTIFHEFG FRGNHVQAQL GQYPYTLTSN PASLEDLQRR DLTYYWEVIL DLTKRALAAS GGEELRNEFR ALAALERTLG LAEGALTRLA PATHGALPAF TRSNVIVIDE AGLLGRHLLT AVVYCWWMIN ALYHTPQYAA RLRPVLVCVG SPTQTASLES TFEHQKLRCS VRQSENVLTY LICNRTLREY ARLSYSWAIF INNKRCVEHE FGNLMKVLEY GLPITEEHMQ FVDRFVVPEN YITNPANLPG WTRLFSSHKE VSAYMAKLHA YLKVTREGEF VVFTLPVLTF VSVKEFDEYR RLTHQPGLTI EKWLTANASR ITNYSQSQDQ DAGHMRCEVH SKQQLVVARN DVTYVLNSQI AVTARLRKLV FGFSGTFRAF EAVLRDDSFV KTQGETSVEF AYRFLSRLIF SGLISFYNFL QRPGLDATQR TLAYARMGEL TAEILSLRPK SSGVPTQASV MADAGAPGER AFDFKQLGPR DGGPDDFPDD DLDVIFAGLD EQQLDVFYCH YTPGEPETTA AVHTQFALLK RAFLGRFRIL QELFGEAFEV APFSTYVDNV IFRGCEMLTG SPRGGLMSVA LQTDNYTLMG YTYARVFAFA DELRRRHATA NVAELLEEAP LPYVVLRDQH GFMSVVNTNI SEFVESIDST ELAMAINADY GISSKLAMTI TRSQGLSLDK VAICFTPGNL RLNSAYVAMS RTTSSEFLRM NLNPLRERHE RDDVISEHIL SALRDPNVVI VY

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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

Concentration0.3 mg/mL
BufferpH: 7.4
Details: 20mM HEPES, 140mM NaCl, 6% glycerol, 0.5mM TCEP, 10mM MgCl2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1309223
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 120337
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL

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