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- PDB-7luf: HSV1 polymerase ternary complex with dsDNA and PNU-183792 -

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Basic information

Entry
Database: PDB / ID: 7luf
TitleHSV1 polymerase ternary complex with dsDNA and PNU-183792
Components
  • DNA (5'-D(*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
  • DNA (5'-D(P*AP*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*CP*G)-3')
  • DNA polymerase
KeywordsTransferase/DNA / Herpesvirus / B-family Polymerase / Nucleotide competing inhibitor / non-nucleoside inhibitor / REPLICATION / Transferase-DNA complex
Function / homology
Function and homology information


viral DNA genome replication / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / host cell nucleus / DNA binding
Similarity search - Function
DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain ...DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-YE4 / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHayes, R.P. / Klein, D.
CitationJournal: Nat Commun / Year: 2021
Title: Structural understanding of non-nucleoside inhibition in an elongating herpesvirus polymerase.
Authors: Hayes, R.P. / Heo, M.R. / Mason, M. / Reid, J. / Burlein, C. / Armacost, K.A. / Tellers, D.M. / Raheem, I. / Shaw, A.W. / Murray, E. / McKenna, P.M. / Abeywickrema, P. / Sharma, S. / Soisson, S.M. / Klein, D.
History
DepositionFeb 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
C: DNA (5'-D(P*AP*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*CP*G)-3')
D: DNA (5'-D(*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
B: DNA polymerase
E: DNA (5'-D(P*AP*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*CP*G)-3')
F: DNA (5'-D(*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,8928
Polymers290,0406
Non-polymers8522
Water00
1
A: DNA polymerase
C: DNA (5'-D(P*AP*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*CP*G)-3')
D: DNA (5'-D(*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4464
Polymers145,0203
Non-polymers4261
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-39 kcal/mol
Surface area48790 Å2
MethodPISA
2
B: DNA polymerase
E: DNA (5'-D(P*AP*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*CP*G)-3')
F: DNA (5'-D(*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4464
Polymers145,0203
Non-polymers4261
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-38 kcal/mol
Surface area49580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.300, 181.300, 233.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 60 through 79 or (resid 80...
21(chain B and (resid 60 through 99 or (resid 100...
12chain C
22chain E
13chain D
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYPROPRO(chain A and (resid 60 through 79 or (resid 80...AA60 - 7926 - 45
121ARGARGARGARG(chain A and (resid 60 through 79 or (resid 80...AA8046
131THRTHRHISHIS(chain A and (resid 60 through 79 or (resid 80...AA59 - 119725 - 1163
141THRTHRHISHIS(chain A and (resid 60 through 79 or (resid 80...AA59 - 119725 - 1163
151THRTHRHISHIS(chain A and (resid 60 through 79 or (resid 80...AA59 - 119725 - 1163
161THRTHRHISHIS(chain A and (resid 60 through 79 or (resid 80...AA59 - 119725 - 1163
211GLYGLYLEULEU(chain B and (resid 60 through 99 or (resid 100...BD60 - 9926 - 65
221LYSLYSLYSLYS(chain B and (resid 60 through 99 or (resid 100...BD10066
231ASNASNHISHIS(chain B and (resid 60 through 99 or (resid 100...BD43 - 11979 - 1163
241ASNASNHISHIS(chain B and (resid 60 through 99 or (resid 100...BD43 - 11979 - 1163
251ASNASNHISHIS(chain B and (resid 60 through 99 or (resid 100...BD43 - 11979 - 1163
261ASNASNHISHIS(chain B and (resid 60 through 99 or (resid 100...BD43 - 11979 - 1163
112DADADGDGchain CCB-12 - 52 - 19
212DADADGDGchain EEE-12 - 52 - 19
113DCDCDCDCchain DDC-13 - 19 - 23
213DCDCDCDCchain FFF-13 - 19 - 23

NCS ensembles :
ID
1
2
3

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Components

#1: Protein DNA polymerase


Mass: 129636.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I7GY94, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(P*AP*TP*GP*GP*TP*AP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*CP*G)-3')


Mass: 8461.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*TP*AP*C)-3')


Mass: 6921.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-YE4 / N-(4-chlorobenzyl)-1-methyl-6-(morpholinomethyl)-4-oxo-1,4-dihydroquinoline-3-carboxamide


Mass: 425.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 6.62 Å3/Da / Density % sol: 81.42 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na HEPES pH 6.8 and 0.4-0.7 M disodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→181.3 Å / Num. obs: 94834 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Net I/σ(I): 8
Reflection shellResolution: 3.5→3.56 Å / Num. unique obs: 4777 / CC1/2: 0.702

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GV9

2gv9


Resolution: 3.5→57.33 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 4710 4.97 %
Rwork0.2258 90012 -
obs0.2268 94722 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 265 Å2 / Biso mean: 109.9042 Å2 / Biso min: 39.21 Å2
Refinement stepCycle: final / Resolution: 3.5→57.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16121 1350 60 0 17531
Biso mean--82.68 --
Num. residues----2164
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9148X-RAY DIFFRACTION13.887TORSIONAL
12B9148X-RAY DIFFRACTION13.887TORSIONAL
21C354X-RAY DIFFRACTION13.887TORSIONAL
22E354X-RAY DIFFRACTION13.887TORSIONAL
31D292X-RAY DIFFRACTION13.887TORSIONAL
32F292X-RAY DIFFRACTION13.887TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.540.33281800.310829833163100
3.54-3.580.31411920.302629313123100
3.58-3.630.33751300.302630393169100
3.63-3.670.33991350.303429853120100
3.67-3.720.28451540.300630353189100
3.72-3.770.31641270.281130323159100
3.77-3.820.29211490.289629843133100
3.82-3.880.31421870.279629423129100
3.88-3.940.2711710.265730343205100
3.94-4.010.29121630.263429493112100
4.01-4.080.27271760.261429733149100
4.08-4.150.30491390.262630083147100
4.15-4.230.3051470.25830423189100
4.23-4.320.29641500.24829843134100
4.32-4.410.26351840.236229823166100
4.41-4.510.25071690.218329793148100
4.51-4.620.24651540.220130143168100
4.62-4.750.23781590.213629673126100
4.75-4.890.20551370.202230203157100
4.89-5.050.22291500.208130143164100
5.05-5.230.20481540.216330033157100
5.23-5.440.24381530.224229983151100
5.44-5.680.25041380.229430543192100
5.68-5.980.25021810.231829803161100
5.98-6.360.25931600.232429733133100
6.36-6.850.26221610.235430213182100
6.85-7.530.20811650.203130343199100
7.54-8.620.2051350.186830423177100
8.62-10.850.15011560.147830173173100
10.85-57.330.21751540.19512993314798

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