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- PDB-5ixa: HCMV DNA polymerase processivity subunit UL44 at neutral pH and l... -

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Basic information

Entry
Database: PDB / ID: 5ixa
TitleHCMV DNA polymerase processivity subunit UL44 at neutral pH and low salt
ComponentsDNA polymerase processivity factor
KeywordsREPLICATION / HCMV Pol accessory subunit / protein-protein interaction / human cytomegalovirus / DNA polymerase / processivity factor
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / : / DNA polymerase processivity factor activity / virion component / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA replication / host cell nucleus / DNA binding
Similarity search - Function
Herpesvirus polymerase accessory protein / Herpesvirus polymerase accessory protein / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / : / Alpha Beta
Similarity search - Domain/homology
DNA polymerase processivity factor
Similarity search - Component
Biological speciesHuman cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.684 Å
AuthorsChen, H. / Coen, D.M. / Hogle, J.M. / Filman, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI19838 United States
CitationJournal: ACS Infect Dis / Year: 2017
Title: A Small Covalent Allosteric Inhibitor of Human Cytomegalovirus DNA Polymerase Subunit Interactions.
Authors: Chen, H. / Coseno, M. / Ficarro, S.B. / Mansueto, M.S. / Komazin-Meredith, G. / Boissel, S. / Filman, D.J. / Marto, J.A. / Hogle, J.M. / Coen, D.M.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase processivity factor
B: DNA polymerase processivity factor


Theoretical massNumber of molelcules
Total (without water)65,1532
Polymers65,1532
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-15 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.026, 100.829, 109.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase processivity factor / Polymerase accessory protein / PAP / Protein ICP36


Mass: 32576.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus (strain AD169) / Strain: AD169 / Gene: UL44 / Production host: Escherichia coli (E. coli) / References: UniProt: P16790
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THAT THE SER 205 IS INDEED CORRECT

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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: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 microliter of 8 mg/mL UL44 in the storage buffer (20 mM Tris (PH 7.5), 500 mM NaCl, 0.1 mM EDTA, 2 mM DTT and 5% glycerol) and 0.2 microliter crystallization buffer (0.1 M HEPES (PH 7.0) ...Details: 0.2 microliter of 8 mg/mL UL44 in the storage buffer (20 mM Tris (PH 7.5), 500 mM NaCl, 0.1 mM EDTA, 2 mM DTT and 5% glycerol) and 0.2 microliter crystallization buffer (0.1 M HEPES (PH 7.0) and 18% PEG12K) were mixed and crystallized in sitting drops over the crystallization buffer at room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.684→37.108 Å / Num. obs: 23307 / % possible obs: 98 % / Redundancy: 3.1 % / Rsym value: 0.109 / Net I/σ(I): 10.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T6L

1t6l


Resolution: 2.684→37.108 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 1187 5.09 %
Rwork0.2103 --
obs0.2128 23307 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.684→37.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3925 0 0 98 4023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114003
X-RAY DIFFRACTIONf_angle_d1.5875441
X-RAY DIFFRACTIONf_dihedral_angle_d20.4451462
X-RAY DIFFRACTIONf_chiral_restr0.076657
X-RAY DIFFRACTIONf_plane_restr0.013687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6843-2.80640.36421250.30382649X-RAY DIFFRACTION95
2.8064-2.95430.32391650.27332734X-RAY DIFFRACTION99
2.9543-3.13930.30171490.25192781X-RAY DIFFRACTION99
3.1393-3.38150.31241440.23162787X-RAY DIFFRACTION99
3.3815-3.72160.27321430.22172786X-RAY DIFFRACTION99
3.7216-4.25940.24161550.20142775X-RAY DIFFRACTION98
4.2594-5.36380.21931630.15962797X-RAY DIFFRACTION97
5.3638-37.11170.21041430.18662811X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0129-0.024-0.00810.0405-0.01150.0105-0.02340.05970.1110.0155-0.0167-0.1007-0.0407-0.0143-00.2310.02210.00530.17860.02310.177947.277270.909275.9575
20.03150.0030.04010.01190.00190.0556-0.00520.0070.0649-0.0246-0.0444-0.006-0.06650.0155-0.03480.21490.02070.1290.26140.05580.313950.523374.762573.1392
30.0061-0.0114-0.01560.02660.04290.0849-0.01240.14280.13740.0233-0.0921-0.0105-0.0225-0.1129-0.01160.23760.0672-0.01530.22780.04790.213832.244891.64964.2843
40.01620.017-0.01770.02290.00180.0191-0.02430.0685-0.0042-0.0769-0.0487-0.0408-0.0195-0.0582-0.00050.1203-0.01710.03510.1703-0.04580.178648.74943.015968.7917
50.0169-0.00970.00380.0058-0.00680.0113-0.00240.0368-0.04630.0072-0.02720.00060.03290.0423-00.3269-0.02460.00560.1602-0.04020.270746.160639.010172.3338
60.01820.00710.01440.07250.01120.0142-0.01010.00710.0106-0.0745-0.01950.13290.00360.00150.0150.1651-0.1446-0.01860.189-0.27890.147930.706426.052855.1148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 270 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 118 )
5X-RAY DIFFRACTION5chain 'B' and (resid 119 through 143 )
6X-RAY DIFFRACTION6chain 'B' and (resid 144 through 272 )

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