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- EMDB-65113: Cryo-EM structure of UL9-DNA complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65113
TitleCryo-EM structure of UL9-DNA complex
Map data
Sample
  • Complex: HSV-1 UL9-DNA complex
    • Protein or peptide: Replication origin-binding protein
    • DNA: DNA (5'-D(P*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP*CP*AP*AP*TP*A)-3')
    • DNA: DNA (5'-D(P*TP*AP*TP*TP*GP*GP*GP*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP*AP*CP*GP*CP*T)-3')
KeywordsHelicase ATPase DNA-binding Dimerization / VIRAL PROTEIN/DNA / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / DNA replication origin binding / DNA replication / host cell nucleus / ATP binding
Similarity search - Function
Replication origin-binding protein / Origin of replication 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
Replication origin-binding protein
Similarity search - Component
Biological speciesHuman herpesvirus 1 (strain 17) / Human alphaherpesvirus 1 strain 17
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMa J / Zhang X / Huang C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of UL9-DNA complex
Authors: Ma J / Zhang X / Huang C
History
DepositionJun 20, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65113.png

Downloads & links

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Map

FileDownload / File: emd_65113.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
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 240 pix.
= 196.8 Å		0.82 Å/pix.
x 240 pix.
= 196.8 Å		0.82 Å/pix.
x 240 pix.
= 196.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.08834085 - 0.14615601
Average (Standard dev.)0.00036059538 (±0.004108185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 196.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65113_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65113_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 : HSV-1 UL9-DNA complex

EntireName: HSV-1 UL9-DNA complex
Components
  • Complex: HSV-1 UL9-DNA complex
    • Protein or peptide: Replication origin-binding protein
    • DNA: DNA (5'-D(P*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP*CP*AP*AP*TP*A)-3')
    • DNA: DNA (5'-D(P*TP*AP*TP*TP*GP*GP*GP*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP*AP*CP*GP*CP*T)-3')

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Supramolecule #1: HSV-1 UL9-DNA complex

SupramoleculeName: HSV-1 UL9-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human herpesvirus 1 (strain 17)
Molecular weightTheoretical: 190 kDa/nm

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Macromolecule #1: Replication origin-binding protein

MacromoleculeName: Replication origin-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 97.331781 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK PFVGGAESGD PLGAGRPIGD DECEQYTSSV SLARMLYGGD LAEWVPRVHP KTTIERQQH GPVTFPNASA PTARCVTVVR APMGSGKTTA LIRWLREAIH SPDTSVLVVS CRRSFTQTLA TRFAESGLVD F VTYFSSTN ...String:
MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK PFVGGAESGD PLGAGRPIGD DECEQYTSSV SLARMLYGGD LAEWVPRVHP KTTIERQQH GPVTFPNASA PTARCVTVVR APMGSGKTTA LIRWLREAIH SPDTSVLVVS CRRSFTQTLA TRFAESGLVD F VTYFSSTN YIMNDRPFHR LIVQVESLHR VGPNLLNNYD VLVLDEVMST LGQLYSPTMQ QLGRVDALML RLLRICPRII AM DATANAQ LVDFLCGLRG EKNVHVVVGE YAMPGFSARR CLFLPRLGTE LLQAALRPPG PPSGPSPDAS PEARGATFFG ELE ARLGGG DNICIFSSTV SFAEIVARFC RQFTDRVLLL HSLTPLGDVT TWGQYRVVIY TTVVTVGLSF DPLHFDGMFA YVKP MNYGP DMVSVYQSLG RVRTLRKGEL LIYMDGSGAR SEPVFTPMLL NHVVSSCGQW PAQFSQVTNL LCRRFKGRCD ASACD TSLG RGSRIYNKFR YKHYFERCTL ACLSDSLNIL HMLLTLNCIR VRFWGHDDTL TPKDFCLFLR GVHFDALRAQ RDLREL RCR DPEASLPAQA AETEEVGLFV EKYLRSDVAP AEIVALMRNL NSLMGRTRFI YLALLEACLR VPMATRSSAI FRRIYDH YA TGVIPTINVT GELELVALPP TLNVTPVWEL LCLCSTMAAR LHWDSAAGGS GRTFGPDDVL DLLTPHYDRY MQLVFELG H CNVTDGLLLS EEAVKRVADA LSGCPPRGSV SETDHAVALF KIIWGELFGV QMAKSTQTFP GAGRVKNLTK QTIVGLLDA HHIDHSACRT HRQLYALLMA HKREFAGARF KLRVPAWGRC LRTHSSSANP NADIILEAAL SELPTEAWPM MQGAVNFSTL

UniProtKB: Replication origin-binding protein

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Macromolecule #2: DNA (5'-D(P*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP...

MacromoleculeName: DNA (5'-D(P*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP*CP*AP*AP*TP*A)-3')
type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 6.97651 KDa
SequenceString:
(DA)(DG)(DC)(DG)(DT)(DT)(DC)(DG)(DC)(DA) (DC)(DT)(DT)(DC)(DG)(DT)(DC)(DC)(DC)(DA) (DA)(DT)(DA)

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Macromolecule #3: DNA (5'-D(P*TP*AP*TP*TP*GP*GP*GP*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP...

MacromoleculeName: DNA (5'-D(P*TP*AP*TP*TP*GP*GP*GP*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP*AP*CP*GP*CP*T)-3')
type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 7.145621 KDa
SequenceString:
(DT)(DA)(DT)(DT)(DG)(DG)(DG)(DA)(DC)(DG) (DA)(DA)(DG)(DT)(DG)(DC)(DG)(DA)(DA)(DC) (DG)(DC)(DT)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 110702
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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