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- PDB-10ho: Crystal structure of alkaline nuclease from Herpes simplex virus-1 -

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Basic information

Entry
Database: PDB / ID: 10ho
TitleCrystal structure of alkaline nuclease from Herpes simplex virus-1
ComponentsDeoxyribonuclease
KeywordsVIRAL PROTEIN / Herpes Simplex Virus 1 / Alkaline nuclease / UL12 / UL12.5
Function / homologyACETATE ION / FORMIC ACID / :
Function and homology information
Biological speciesHuman alphaherpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsSharma, N. / Rani, C. / Wright, D.L. / Weller, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI021747-35 United States
CitationJournal: Plos Pathog. / Year: 2026
Title: Viral Nuclease Inhibitors: Small molecule disruptors of the UL12 alkaline nuclease display broad anti-herpes virus activity.
Authors: Sharma, N. / Xie, X. / Szczepaniak, R. / Rani, C. / Khosro, S.K. / Krucinska, J. / Chen, X. / Do, D. / Wright, L. / Wright, D. / Weller, S.
History
DepositionJan 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4535
Polymers58,1601
Non-polymers2934
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.997, 80.233, 127.572
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Deoxyribonuclease


Mass: 58159.625 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: UL12 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140GKD1

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Non-polymers , 5 types, 69 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Ammonium sulfate, Sodium acetate, PEG 4000, Glycerol and DMSO
PH range: 4.6-5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 11, 2024 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.46→29.642 Å / Num. obs: 22700 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.037 / Rrim(I) all: 0.052 / Χ2: 0.85 / Net I/av σ(I): 12.4 / Net I/σ(I): 13.8
Reflection shellResolution: 2.46→2.56 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2508 / CC1/2: 0.885 / Rpim(I) all: 0.446 / Rsym value: 0.316 / Χ2: 0.77 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
FAST_DPdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→29.642 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.024 / SU ML: 0.213 / Cross valid method: FREE R-VALUE / ESU R: 0.296 / ESU R Free: 0.236
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2378 1104 4.875 %
Rwork0.1809 21540 -
all0.184 --
obs-22644 99.876 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.938 Å2
Baniso -1Baniso -2Baniso -3
1-7.233 Å2-0 Å20 Å2
2---3 Å20 Å2
3----4.233 Å2
Refinement stepCycle: LAST / Resolution: 2.46→29.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 18 65 3400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123422
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163226
X-RAY DIFFRACTIONr_angle_refined_deg2.2471.8284655
X-RAY DIFFRACTIONr_angle_other_deg0.7541.7467411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3195418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.319536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50910525
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.3910150
X-RAY DIFFRACTIONr_chiral_restr0.0990.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02821
X-RAY DIFFRACTIONr_nbd_refined0.2290.2706
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.22944
X-RAY DIFFRACTIONr_nbtor_refined0.1920.21636
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1850.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3260.26
X-RAY DIFFRACTIONr_nbd_other0.1510.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0380.23
X-RAY DIFFRACTIONr_mcbond_it7.2985.8121691
X-RAY DIFFRACTIONr_mcbond_other7.2995.8121692
X-RAY DIFFRACTIONr_mcangle_it10.02410.3962102
X-RAY DIFFRACTIONr_mcangle_other10.02110.4012103
X-RAY DIFFRACTIONr_scbond_it8.9456.5521731
X-RAY DIFFRACTIONr_scbond_other8.846.5391728
X-RAY DIFFRACTIONr_scangle_it12.45811.6322553
X-RAY DIFFRACTIONr_scangle_other12.39911.6112548
X-RAY DIFFRACTIONr_lrange_it13.98955.1313699
X-RAY DIFFRACTIONr_lrange_other14.00455.1473696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.46-2.5230.364750.32715460.32916220.8990.999.93830.307
2.523-2.5920.303680.27115310.27216000.9410.93499.93750.244
2.592-2.6670.297840.24814600.25115450.9340.94899.93530.224
2.667-2.7480.258720.22114310.22315030.9520.9641000.197
2.748-2.8370.312790.21913930.22414720.9280.9661000.199
2.837-2.9360.305600.20713640.21114240.9180.9661000.188
2.936-3.0460.259620.20413100.20613720.9530.971000.182
3.046-3.1690.276710.18512460.1913170.9440.9761000.169
3.169-3.3080.285610.212250.20412860.9490.9731000.19
3.308-3.4670.306640.20311590.20812230.9510.9751000.192
3.467-3.6520.246540.20211060.20411600.9540.9781000.194
3.652-3.870.225600.18710560.18911160.9690.9821000.182
3.87-4.1320.256450.1559900.15910350.9590.9861000.155
4.132-4.4560.167530.1249360.1269890.9830.9911000.127
4.456-4.870.18390.1198670.1219070.9810.99299.88970.127
4.87-5.4260.198410.1617780.1638230.9760.98699.5140.171
5.426-6.2310.217470.1567030.167500.9690.9851000.162
6.231-7.5490.216300.1486090.1516390.9780.9871000.163
7.549-10.3450.163200.134940.1315150.9830.9999.80580.156
10.345-29.6420.202190.2443270.2413460.9750.9571000.292

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