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- EMDB-74190: The complex of HSV-1 proteins UL9 and ICP8 with forked DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-74190
TitleThe complex of HSV-1 proteins UL9 and ICP8 with forked DNA
Map datacomposite map
Sample
  • Complex: The complex of HSV-1 proteins UL9 and ICP8 with forked DNA
    • Protein or peptide: Major DNA-binding protein
    • Protein or peptide: Replication origin-binding protein
    • DNA: DNA (40-MER)
    • DNA: DNA (31-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsDNA replication / protein-DNA complex / REPLICATION-DNA complex
Function / homology
Function and homology information


nuclear viral factory / bidirectional double-stranded viral DNA replication / DNA replication origin binding / single-stranded DNA binding / DNA replication / host cell nucleus / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
Replication origin-binding protein / Origin of replication binding protein / Viral ssDNA-binding protein / DBP-like superfamily / Viral ssDNA binding protein, head domain / ssDNA binding protein / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Major DNA-binding protein / Replication origin-binding protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain 17
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBaranovskiy AG / Morstadt LM / Romero EE / Babayeva ND / Tahirov TH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM152032 United States
CitationJournal: To Be Published
Title: Structural basis for unwinding the origins of HSV-1 genome by cooperative action of viral proteins UL9 and ICP8
Authors: Baranovskiy AG / Morstadt LM / Romero EE / Babayeva ND / Tahirov TH
History
DepositionDec 2, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74190.png

Downloads & links

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Map

FileDownload / File: emd_74190.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.15 Å/pix.
x 280 pix.
= 322.56 Å		1.15 Å/pix.
x 280 pix.
= 322.56 Å		1.15 Å/pix.
x 280 pix.
= 322.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.152 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-39.353650000000002 - 56.067419999999998
Average (Standard dev.)0.00055487745 (±1.0904245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The complex of HSV-1 proteins UL9 and ICP8 with forked DNA

EntireName: The complex of HSV-1 proteins UL9 and ICP8 with forked DNA
Components
  • Complex: The complex of HSV-1 proteins UL9 and ICP8 with forked DNA
    • Protein or peptide: Major DNA-binding protein
    • Protein or peptide: Replication origin-binding protein
    • DNA: DNA (40-MER)
    • DNA: DNA (31-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: The complex of HSV-1 proteins UL9 and ICP8 with forked DNA

SupramoleculeName: The complex of HSV-1 proteins UL9 and ICP8 with forked DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human alphaherpesvirus 1 strain 17

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Macromolecule #1: Major DNA-binding protein

MacromoleculeName: Major DNA-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 128.486539 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: METKPKTATT IKVPPGPLGY VYARACPSEG IELLALLSAR SGDSDVAVAP LVVGLTVESG FEANVAVVVG SRTTGLGGTA VSLKLTPSH YSSSVYVFHG GRHLDPSTQA PNLTRLCERA RRHFGFSDYT PRPGDLKHET TGEALCERLG LDPDRALLYL V VTEGFKEA ...String:
METKPKTATT IKVPPGPLGY VYARACPSEG IELLALLSAR SGDSDVAVAP LVVGLTVESG FEANVAVVVG SRTTGLGGTA VSLKLTPSH YSSSVYVFHG GRHLDPSTQA PNLTRLCERA RRHFGFSDYT PRPGDLKHET TGEALCERLG LDPDRALLYL V VTEGFKEA VCINNTFLHL GGSDKVTIGG AEVHRIPVYP LQLFMPDFSR VIAEPFNANH RSIGEKFTYP LPFFNRPLNR LL FEAVVGP AAVALRCRNV DAVARAAAHL AFDENHEGAA LPADITFTAF EASQGKTPRG GRDGGGKGAA GGFEQRLASV MAG DAALAL ESIVSMAVFD EPPTDISAWP LFEGQDTAAA RANAVGAYLA RAAGLVGAMV FSTNSALHLT EVDDAGPADP KDHS KPSFY RFFLVPGTHV AANPQVDREG HVVPGFEGRP TAPLVGGTQE FAGEHLAMLC GFSPALLAKM LFYLERCDGA VIVGR QEMD VFRYVADSNQ TDVPCNLCTF DTRHACVHTT LMRLRARHPK FASAARGAIG VFGTMNSMYS DCDVLGNYAA FSALKR ADG SETARTIMQE TYRAATERVM AELETLQYVD QAVPTAMGRL ETIITNREAL HTVVNNVRQV VDREVEQLMR NLVEGRN FK FRDGLGEANH AMSLTLDPYA CGPCPLLQLL GRRSNLAVYQ DLALSQCHGV FAGQSVEGRN FRNQFQPVLR RRVMDMFN N GFLSAKTLTV ALSEGAAICA PSLTAGQTAP AESSFEGDVA RVTLGFPKEL RVKSRVLFAG ASANASEAAK ARVASLQSA YQKPDKRVDI LLGPLGFLLK QFHAAIFPNG KPPGSNQPNP QWFWTALQRN QLPARLLSRE DIETIAFIKK FSLDYGAINF INLAPNNVS ELAMYYMANQ ILRYCDHSTY FINTLTAIIA GSRRPPSVQA AAAWSAQGGA GLEAGARALM DAVDAHPGAW T SMFASCNL LRPVMAARPM VVLGLSISKY YGMAGNDRVF QAGNWASLMG GKNACPLLIF DRTRKFVLAC PRAGFVCAAS SL GGGAHES SLCEQLRGII SEGGAAVASS VFVATVKSLG PRTQQLQIED WLALLEDEYL SEEMMELTAR ALERGNGEWS TDA ALEVAH EAEALVSQLG NAGEVFNFGD FGCEDDNATP FGGPGAPGPA FAGRKRAFHG DDPFGEGPPD KKGDLTLDML

UniProtKB: Major DNA-binding protein

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Macromolecule #2: Replication origin-binding protein

MacromoleculeName: Replication origin-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 94.371672 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPFVGGAESG DPLGAGRPIG DDECEQYTSS VSLARMLYGG DLAEWVPRVH PKTTIERQQH GPVTFPNASA PTARCVTVVR APMGSGKTT ALIRWLREAI HSPDTSVLVV SCRRSFTQTL ATRFAESGLV DFVTYFSSTN YIMNDRPFHR LIVQVESLHR V GPNLLNNY ...String:
MPFVGGAESG DPLGAGRPIG DDECEQYTSS VSLARMLYGG DLAEWVPRVH PKTTIERQQH GPVTFPNASA PTARCVTVVR APMGSGKTT ALIRWLREAI HSPDTSVLVV SCRRSFTQTL ATRFAESGLV DFVTYFSSTN YIMNDRPFHR LIVQVESLHR V GPNLLNNY DVLVLDEVMS TLGQLYSPTM QQLGRVDALM LRLLRICPRI IAMDATANAQ LVDFLCGLRG EKNVHVVVGE YA MPGFSAR RCLFLPRLGT ELLQAALRPP GPPSGPSPDA SPEARGATFF GELEARLGGG DNICIFSSTV SFAEIVARFC RQF TDRVLL LHSLTPLGDV TTWGQYRVVI YTTVVTVGLS FDPLHFDGMF AYVKPMNYGP DMVSVYQSLG RVRTLRKGEL LIYM DGSGA RSEPVFTPML LNHVVSSCGQ WPAQFSQVTN LLCRRFKGRC DASACDTSLG RGSRIYNKFR YKHYFERCTL ACLSD SLNI LHMLLTLNCI RVRFWGHDDT LTPKDFCLFL RGVHFDALRA QRDLRELRCR DPEASLPAQA AETEEVGLFV EKYLRS DVA PAEIVALMRN LNSLMGRTRF IYLALLEACL RVPMATRSSA IFRRIYDHYA TGVIPTINVT GELELVALPP TLNVTPV WE LLCLCSTMAA RLHWDSAAGG SGRTFGPDDV LDLLTPHYDR YMQLVFELGH CNVTDGLLLS EEAVKRVADA LSGCPPRG S VSETDHAVAL FKIIWGELFG VQMAKSTQTF PGAGRVKNLT KQTIVGLLDA HHIDHSACRT HRQLYALLMA HKREFAGAR FKLRVPAWGR CLRTHSSSAN PNADIILEAA LSELPTEAWP MMQGAVNFST L

UniProtKB: Replication origin-binding protein

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Macromolecule #3: DNA (40-MER)

MacromoleculeName: DNA (40-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 12.184867 KDa
SequenceString:
(DC)(DG)(DA)(DA)(DG)(DC)(DG)(DT)(DT)(DC) (DG)(DC)(DA)(DC)(DT)(DT)(DC)(DG)(DT)(DC) (DC)(DC)(DA)(DA)(DT)(DC)(DT)(DA)(DA) (DC)(DA)(DA)(DT)(DA)(DT)(DC)(DA)(DA)(DT) (DA)

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Macromolecule #4: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 9.579201 KDa
SequenceString:
(DA)(DT)(DA)(DC)(DA)(DA)(DT)(DC)(DA)(DA) (DG)(DG)(DA)(DC)(DG)(DA)(DA)(DG)(DT)(DG) (DC)(DG)(DA)(DA)(DC)(DG)(DC)(DT)(DT) (DC)(DG)

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 411805
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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