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 9YCP | pdb_00009ycp

HSV Helicase-primase complex bound to IM-250


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9YCP

This is version 1.1 of the entry. See complete history. 

Literature

Mechanisms of HSV-1 helicase-primase inhibition and replication fork complex assembly.

Yu, Z., Sathyanarayana, P., Liu, C., Tan, J.M.J., Yang, P., Das, B., Hu, S., Fan, X., Ji, C., Weller, S.K., Shekhar, M., Coen, D.M., Kranzusch, P.J., Loparo, J.J., Abraham, J.

(2026) Cell 189: 478-494.e18

  • DOI: https://doi.org/10.1016/j.cell.2025.11.041
  • Primary Citation Related Structures: 
    9YC9, 9YCP, 9YCT, 9YCV

  • PubMed Abstract: 

    Herpesviruses are widespread double-stranded DNA viruses that establish lifelong latency and cause various diseases. Although DNA-polymerase-targeting antivirals are effective, increasing drug resistance underscores the need for alternatives. Helicase-primase inhibitors (HPIs) are promising antivirals, but their mechanisms of action are poorly defined. Furthermore, how the helicase-primase (H/P) complex and DNA polymerase coordinate genome replication is not well understood for herpesviruses. Here, we report cryo-electron microscopy (cryo-EM) structures of the herpes simplex virus 1 H/P complex bound to HPIs, showing that these lock the H/P complex in an inactive state. Single-molecule assays reveal that HPIs cause H/P complexes to pause in unwinding activity on DNA. The structure of an HPI-bound replication fork complex, comprising the H/P complex (UL5, UL52, and UL8) and the polymerase holoenzyme (UL30 and UL42), reveals a previously uncharacterized interface bridging these complexes. These findings provide a structural framework for understanding herpesvirus replisome assembly and advancing inhibitor development.


  • Organizational Affiliation: 
    • Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 295.67 kDa 
  • Atom Count: 15,394 
  • Modeled Residue Count: 1,977 
  • Deposited Residue Count: 2,696 
  • Unique protein chains: 3
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
UL52B [auth C]1,058Human alphaherpesvirus 1 strain R-15Mutation(s): 0 
Gene Names: UL52
EC: 2.7.7
UniProt
Find proteins for A0A5J6DWG4 (Human herpesvirus 1)
Explore A0A5J6DWG4 
Go to UniProtKB:  A0A5J6DWG4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5J6DWG4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
UL5C [auth A]882Human alphaherpesvirus 1 strain R-15Mutation(s): 0 
Gene Names: UL5
EC: 3.6.4
UniProt
Find proteins for A0A5J6DVR7 (Human herpesvirus 1)
Explore A0A5J6DVR7 
Go to UniProtKB:  A0A5J6DVR7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5J6DVR7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
UL8D [auth B]750Human alphaherpesvirus 1 strain R-15Mutation(s): 0 
Gene Names: UL8
UniProt
Find proteins for P10192 (Human herpesvirus 1 (strain 17))
Explore P10192 
Go to UniProtKB:  P10192
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10192
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')A [auth D]6Human alphaherpesvirus 1 strain R-15
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CHB
(Subject of Investigation/LOI)

Query on A1CHB



Download:Ideal Coordinates CCD File
F [auth C]N-{5-[(R)-amino(hydroxy)(methyl)-lambda~4~-sulfanyl]-4-methyl-1,3-thiazol-2-yl}-2-(2',5'-difluoro[1,1'-biphenyl]-4-yl)-N-methylacetamide
C20 H21 F2 N3 O2 S2
XMZIBPDSCWYNDP-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-31
    Type: Initial release
  • Version 1.1: 2026-07-15
    Changes: Data collection, Database references