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- PDB-5iwd: HCMV DNA polymerase subunit UL44 complex with a small molecule -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5iwd
TitleHCMV DNA polymerase subunit UL44 complex with a small molecule
ComponentsDNA polymerase processivity factor
KeywordsREPLICATION/REPLICATION INHIBITOR / covalent inhibitor / HCMV Pol accessory subunit / protein-protein interaction / human cytomegalovirus / DNA polymerase / processivity factor / REPLICATION-REPLICATION INHIBITOR complex
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 / virus-mediated perturbation of host defense response / 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
Chem-6EV / DNA polymerase processivity factor
Similarity search - Component
Biological speciesHuman cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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)R01 AI019838 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 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase processivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2154
Polymers32,5901
Non-polymers6253
Water181
1
A: DNA polymerase processivity factor
hetero molecules

A: DNA polymerase processivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4318
Polymers65,1812
Non-polymers1,2506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area1620 Å2
ΔGint-14 kcal/mol
Surface area27210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.801, 127.041, 66.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 32590.490 Da / Num. of mol.: 1
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: Chemical ChemComp-6EV / 5-methylidene-3-(methylsulfanyl)-2-benzothiophen-4(5H)-one


Mass: 208.300 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H8OS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsauthors have indicated that the correct residue in this position is a Ser

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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: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 uL of 10 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 1 uL crystallization buffer (75 mM ammonium sulfate, 50 mM HEPES (pH ...Details: 1 uL of 10 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 1 uL crystallization buffer (75 mM ammonium sulfate, 50 mM HEPES (pH 7.5) and 10% PEG4K) were mixed in hanging drops. Crystals were obtained by vapor diffusion over a 1.8 M NaCl solution, after one day

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 12483 / % possible obs: 98 % / Redundancy: 3 % / Rsym value: 0.038 / Net I/σ(I): 27.1
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BD1YYP

Resolution: 2.56→27.122 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.267 600 4.81 %RANDOM
Rwork0.2125 ---
obs0.215 12465 97.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→27.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 39 1 2095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082150
X-RAY DIFFRACTIONf_angle_d1.1022925
X-RAY DIFFRACTIONf_dihedral_angle_d18.2971343
X-RAY DIFFRACTIONf_chiral_restr0.063340
X-RAY DIFFRACTIONf_plane_restr0.006369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5603-2.81770.32711680.27642882X-RAY DIFFRACTION98
2.8177-3.22480.30881580.25512989X-RAY DIFFRACTION100
3.2248-4.06070.28121260.22943028X-RAY DIFFRACTION99
4.0607-27.12330.24431480.18922966X-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)
12.5182.1743-0.7560.6978-0.88951.65710.1923-0.13890.17010.3822-0.08050.22350.3936-0.1580.01060.5002-0.0307-0.04190.4107-0.16310.387634.061436.5981-7.3769
22.3390.34950.29211.3592-0.75682.4858-0.04220.32720.15490.1216-0.0576-0.01970.07490.083-0.00020.7033-0.04020.00350.6425-0.04110.648335.086835.9833-11.0024
31.99012.44610.14321.3056-1.85340.08080.10230.18950.0960.39620.3130.7453-0.37520.038-0.00820.76070.03590.10920.8040.01180.816716.017516.734-6.2358
42.16580.2708-0.57673.1952-2.55261.53130.03160.0839-0.20230.23510.41240.8774-0.44880.02830.01480.55090.02660.10780.67870.04310.854913.882213.274-3.1737
5-0.29760.37280.5215-0.64180.28551.41780.26280.5172-0.88590.53331.52110.5919-1.2748-0.3150.61860.5917-0.1219-0.17751.06980.26821.089512.896416.8965-14.4486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 185 )
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 260 )
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 276 )

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