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9yct

HSV helicase-primase complex bound to pritelivir

Method: ELECTRON MICROSCOPY Dmax: 174.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

UL52

Human alphaherpesvirus 1 strain R-15

UniProt A0A5J6DWG4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain C； UniProt 1–1058 Not recorded ;DNA (5'-D(*TP*TP*TP*TP*TP*T)-3') ; × 1 UL5 × 1 （A0A5J6DVR7） UL8 × 1 （P10192） ZN ZINC ION × 1 A1BXB Pritelivir × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YCT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9YC9 HSV replication fork complex bound to pritelivir Deposited 2025-09-18 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: octameric
Chain C 1–1058（1058 aa）
Not recorded ZN ZINC ION × 1 A1BXB Pritelivir × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9YCP HSV Helicase-primase complex bound to IM-250 Deposited 2025-09-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain C 1–1058（1058 aa）
Not recorded ZN ZINC ION × 1 A1CHB 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 × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9YCV HSV Helicase-primase complex bound to amenamevir Deposited 2025-09-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain C 1–1058（1058 aa）
Not recorded ZN ZINC ION × 1 A1BXD Amenamevir × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A5J6DWG4_HHV1
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–1058； UniProt 1–1058

UL5

Human alphaherpesvirus 1 strain R-15

UniProt A0A5J6DVR7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain A； UniProt 1–882 Not recorded ;DNA (5'-D(*TP*TP*TP*TP*TP*T)-3') ; × 1 UL52 × 1 （A0A5J6DWG4） UL8 × 1 （P10192） ZN ZINC ION × 1 A1BXB Pritelivir × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YCT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9YC9 HSV replication fork complex bound to pritelivir Deposited 2025-09-18 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: octameric
Chain A 1–882（882 aa）
Not recorded ZN ZINC ION × 1 A1BXB Pritelivir × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9YCP HSV Helicase-primase complex bound to IM-250 Deposited 2025-09-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain A 1–882（882 aa）
Not recorded ZN ZINC ION × 1 A1CHB 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 × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9YCV HSV Helicase-primase complex bound to amenamevir Deposited 2025-09-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain A 1–882（882 aa）
Not recorded ZN ZINC ION × 1 A1BXD Amenamevir × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A5J6DVR7_HHV1
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–882； UniProt 1–882

UL8

Human alphaherpesvirus 1 strain R-15

UniProt P10192

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain B； UniProt 1–750 Not recorded ;DNA (5'-D(*TP*TP*TP*TP*TP*T)-3') ; × 1 UL52 × 1 （A0A5J6DWG4） UL5 × 1 （A0A5J6DVR7） ZN ZINC ION × 1 A1BXB Pritelivir × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YCT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9NDA The rigid portion of Cryo-EM structure of Herpesvirus Helicase-Primase complex with amenamevir Deposited 2025-02-17 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–750（750 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9NDQ The rigid portion of Cryo-EM structure of Herpesvirus Helicase-Primase complex prepared with forked DNA and ATP-gamma-S Deposited 2025-02-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–750（750 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9NDZ The rigid portion of Cryo-EM structure of Herpesvirus Helicase-Primase complex prepared with forked DNA, ATP-gamma-S and Pritelivir Deposited 2025-02-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–750（750 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9NEB The rigid portion of Cryo-EM structure of Herpesvirus Helicase-Primase complex with Pritelivir Deposited 2025-02-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–750（750 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9NN2 Composite structure of HSV-1 helicase-primase in complex with a forked DNA and amenamevir Deposited 2025-03-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain C 1–750（750 aa）
Not recorded A1BXD Amenamevir × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；CHAPSO is made fresh at 80 mM before being added to the sample at a final concentration of 2 mM immediately before vitrification
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9NNP Composite structure of HSV-1 helicase-primase in complex with a forked DNA Deposited 2025-03-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain C 1–750（750 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；CHAPSO is made fresh at 80 mM before being added to the sample at a final concentration of 4 mM immediately before vitrification
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9NQP Composite structure of HSV1 helicase-primase in complex with a forked DNA and pritelivir Deposited 2025-03-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain C 1–750（750 aa）
Not recorded A1BXB Pritelivir × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；CHAPSO is made fresh at 80 mM before being added to the sample at a final concentration of 2 mM immediately before vitrification
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9UT1 The helicase-primase complex from HHV1 bound with ssDNA and amenamevir Deposited 2025-05-02 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: tetrameric
Chain C 1–750（750 aa）
Mutation：R64T/R71E A1BXD Amenamevir × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9UT4 The primase module of the helicase-primase complex from HHV1 bound with ssDNA and amenamevir Deposited 2025-05-02 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–750（750 aa）
Mutation：R64T/R71E No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
9UT5 The helicase-primase complex from HHV1 bound with ssDNA and pritelivir Deposited 2025-05-02 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: tetrameric
Chain C 1–750（750 aa）
Mutation：R64T/R71E A1BXB Pritelivir × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9UT7 The Primase module of the helicase-primase complex from HHV1 bound with ssDNA and pritelivir Deposited 2025-05-02 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–750（750 aa）
Mutation：R64T/R71E No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
9YC9 HSV replication fork complex bound to pritelivir Deposited 2025-09-18 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: octameric
Chain B 1–750（750 aa）
Not recorded ZN ZINC ION × 1 A1BXB Pritelivir × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9YCP HSV Helicase-primase complex bound to IM-250 Deposited 2025-09-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–750（750 aa）
Not recorded ZN ZINC ION × 1 A1CHB 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 × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9YCV HSV Helicase-primase complex bound to amenamevir Deposited 2025-09-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–750（750 aa）
Not recorded ZN ZINC ION × 1 A1BXD Amenamevir × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HEPA_HHV11
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 1–750； UniProt 1–750

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9yct

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9yct
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9yct
Deposition date deposition_date2025-09-19
Structure title titleHSV helicase-primase complex bound to pritelivir
Keywords keywordsHSV, helicase-primase, pritelivir, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier51.49 Å
Radius of gyration Rg (electron density) rg_electron51.62 Å
Forward intensity I(0) i01899710000.00
Molecular weight molecular_weight240040.0 kDa
Excluded volume excluded_volume231750 ų
Envelope volume envelope_volume469510 ų
Hydration-shell volume shell_volume78536 ų
Envelope diameter envelope_diameter188.6 Å
Shell Rg shell_rg52.40 Å
Envelope Rg envelope_rg50.49 Å
Shape Rg shape_rg51.66 Å
Total Rg total_rg51.58 Å
Total atoms total_atoms18212
Residues n_residues2338
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax174.5 Å
Rg (real space) rg_real53.73 Å
Rg uncertainty (real space) rg_real_error0.81 Å
I(0) (real space) i0_real1.8990e+09
I(0) uncertainty (real space) i0_real_error3.2710e+07
Rg (reciprocal space) rg_reciprocal51.33 Å
I(0) (reciprocal space) i0_reciprocal1899000000.0000
Solution quality estimate total_estimate0.6523
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.7 Å
Skewness Skewness skewness0.477
Kurtosis Kurtosis kurtosis-0.393
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha1.4710
Highest regularization parameter α highest_alpha67830000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 0.879; Sysdev: 0.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.319
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)