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- PDB-9ut1: The helicase-primase complex from HHV1 bound with ssDNA and amenamevir -

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Basic information

Entry
Database: PDB / ID: 9ut1
TitleThe helicase-primase complex from HHV1 bound with ssDNA and amenamevir
Components
  • (Ubiquitin-like protein SMT3,DNA ...) x 2
  • DNA replication helicase
  • synthetic DNA
KeywordsREPLICATION / Helicase / Primase / Inhibitor Complex / Herpesvirus
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / bidirectional double-stranded viral DNA replication / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / helicase activity / condensed nuclear chromosome / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein tag activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA-directed RNA polymerase activity / DNA replication / hydrolase activity / host cell nucleus / zinc ion binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
DNA replication helicase domain / DNA helicase/primase complex-associated protein / DNA replication helicase, Herpesvirus / Herpesvirus DNA helicase/primase complex associated protein / Helicase / DNA primase / Herpesviridae UL52/UL70 DNA primase / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues ...DNA replication helicase domain / DNA helicase/primase complex-associated protein / DNA replication helicase, Herpesvirus / Herpesvirus DNA helicase/primase complex associated protein / Helicase / DNA primase / Herpesviridae UL52/UL70 DNA primase / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA / DNA replication helicase / DNA helicase/primase complex-associated protein / DNA primase / Small ubiquitin-related modifier
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 (Herpes simplex virus type 1)
Saccharomyces cerevisiae S288C (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsSato, K. / Kise, Y. / Hamada, K. / Nureki, O. / Sengoku, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: The helicase-primase complex from HHV1 bound with ssDNA and amenamevir
Authors: Sato, K. / Kise, Y. / Hamada, K. / Nureki, O. / Sengoku, T.
History
DepositionMay 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA replication helicase
B: Ubiquitin-like protein SMT3,DNA primase
C: Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein
D: synthetic DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,2326
Polymers332,6844
Non-polymers5482
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Ubiquitin-like protein SMT3,DNA ... , 2 types, 2 molecules BC

#2: Protein Ubiquitin-like protein SMT3,DNA primase


Mass: 130398.977 Da / Num. of mol.: 1 / Mutation: R64T/R71E
Source method: isolated from a genetically manipulated source
Details: SUMOstar
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast), (gene. exp.) Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Gene: SMT3, YDR510W, D9719.15, UL52 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q12306, UniProt: P10236, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#3: Protein Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein / HEPA / Primase-associated factor


Mass: 95846.422 Da / Num. of mol.: 1 / Mutation: R64T/R71E
Source method: isolated from a genetically manipulated source
Details: SUMOstar
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast), (gene. exp.) Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Gene: SMT3, YDR510W, D9719.15, UL8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12306, UniProt: P10192

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Protein / DNA chain , 2 types, 2 molecules AD

#1: Protein DNA replication helicase


Mass: 104354.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Gene: HELI, UL5 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P10189, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#4: DNA chain synthetic DNA


Mass: 2084.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-A1BXD / Amenamevir


Mass: 482.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N4O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Helicase-primase complex from human herpesvirus 1COMPLEX#1-#40MULTIPLE SOURCES
2helicaseCOMPLEX#11RECOMBINANT
3primaseCOMPLEX#2-#32RECOMBINANT
4ssDNACOMPLEX#43SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Human alphaherpesvirus 1 (Herpes simplex virus type 1)10298
33Saccharomyces cerevisiae S288C (yeast)559292
12Human alphaherpesvirus 1 (Herpes simplex virus type 1)10298
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 49.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction3D-Flex refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 467000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 173.79 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002719457
ELECTRON MICROSCOPYf_angle_d0.747826542
ELECTRON MICROSCOPYf_chiral_restr0.04512997
ELECTRON MICROSCOPYf_plane_restr0.00453437
ELECTRON MICROSCOPYf_dihedral_angle_d6.97022805

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