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- PDB-1yyp: Crystal structure of cytomegalovirus UL44 bound to C-terminal pep... -

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Basic information

Entry
Database: PDB / ID: 1yyp
TitleCrystal structure of cytomegalovirus UL44 bound to C-terminal peptide from CMV UL54
Components
  • DNA polymerase
  • DNA polymerase processivity factor
KeywordsREPLICATION/TRANSFERASE / PROCESSIVITY FOLD (SAME FOLD AS HSV UL42 / PCNA / AND HOMOTRIMERIC SLIDING CLAMPS) / REPLICATION-TRANSFERASE COMPLEX
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / DNA polymerase processivity factor activity / virion component / DNA-templated DNA replication / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / virus-mediated perturbation of host defense response ...bidirectional double-stranded viral DNA replication / DNA polymerase processivity factor activity / virion component / DNA-templated DNA replication / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / virus-mediated perturbation of host defense response / nucleotide binding / 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 / : / 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 ...Herpesvirus polymerase accessory protein / Herpesvirus polymerase accessory protein / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / : / 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 / Alpha Beta
Similarity search - Domain/homology
DNA polymerase catalytic subunit / DNA polymerase processivity factor
Similarity search - Component
Biological speciesHuman herpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsAppleton, B.A. / Brooks, J. / Loregian, A. / Filman, D.J. / Coen, D.M. / Hogle, J.M.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Crystal structure of the cytomegalovirus DNA polymerase subunit UL44 in complex with the C terminus from the catalytic subunit. Differences in structure and function relative to unliganded UL44.
Authors: Appleton, B.A. / Brooks, J. / Loregian, A. / Filman, D.J. / Coen, D.M. / Hogle, J.M.
#1: Journal: Mol.Cell / Year: 2004
Title: The cytomegalovirus DNA polymerase subunit UL44 forms a C clamp-shaped dimer
#2: Journal: J.Virol. / Year: 2004
Title: Specific residues in the connector loop of the human cytomegalovirus DNA polymerase accessory protein UL44 are crucial for interaction with the UL54 catalytic subunit
#3: Journal: J.Virol. / Year: 2004
Title: Residues of human cytomegalovirus DNA polymerase catalytic subunit UL54 that are necessary and sufficient for interaction with the accessory protein UL44
#4: Journal: J.Virol. / Year: 1992
Title: Physical and functional interaction of human cytomegalovirus DNA polymerase and its accessory protein (ICP36) expressed in insect cells
History
DepositionFeb 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AUTHOR STATES THAT THE SER 205 IS INDEED CORRECT AND IT MAY REPRESENT A DIFFERENT ISOLATE ...SEQUENCE AUTHOR STATES THAT THE SER 205 IS INDEED CORRECT AND IT MAY REPRESENT A DIFFERENT ISOLATE CYTOMEGALOVIRUS, REFERRING TO ERTL PF, POWELL KL. "PHYSICAL AND FUNCTIONAL INTERACTION OF HUMAN CYTOMEGALOVIRUS DNA POLYMERASE AND ITS ACCESSORY PROTEIN (ICP36) EXPRESSED IN INSECT CELLS." J VIROL. 1992 JUL;66(7):4126-33.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7329
Polymers35,1622
Non-polymers5707
Water86548
1
A: DNA polymerase processivity factor
B: DNA polymerase
hetero molecules

A: DNA polymerase processivity factor
B: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,46418
Polymers70,3234
Non-polymers1,14114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Unit cell
Length a, b, c (Å)91.787, 127.592, 65.975
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 / ICP36 protein


Mass: 32576.506 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Genus: Cytomegalovirus / Gene: UL44 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P16790
#2: Protein/peptide DNA polymerase / POL


Mass: 2585.077 Da / Num. of mol.: 1 / Fragment: C-TERMINAL 22 RESIDUES / Source method: obtained synthetically / References: UniProt: P08546, DNA-directed DNA polymerase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 2 M ammonium sulfate, 100 mM phosphate-citrate, and 10 mM DTT , pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793, 0.9794, 1.008, 0.9537
DetectorType: SBC-2 / Detector: CCD / Date: Aug 9, 2003
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97941
31.0081
40.95371
ReflectionResolution: 2.5→30 Å / Num. all: 13819 / Num. obs: 13802 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Biso Wilson estimate: 53.1 Å2 / Rmerge(I) obs: 0.058 / Χ2: 0.966 / Net I/σ(I): 44.8
Reflection shellResolution: 2.5→2.61 Å / % possible obs: 100 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 13.7 / Num. measured obs: 1697 / Num. unique all: 1697 / Χ2: 0.771 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
4
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
14 wavelength10.97936.3-8.2
14 wavelength20.95373.61-2.65
14 wavelength30.97943.4-10.8
14 wavelength41.0080.53-3.02
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se52.3860.1270.2410.1521.048
2Se44.1320.0420.2740.1610.829
3Se600.4540.1190.1141.041
4Se40.89900.280.2030.653
Phasing dmFOM : 0.73 / FOM acentric: 0.74 / FOM centric: 0.72 / Reflection: 13733 / Reflection acentric: 12117 / Reflection centric: 1616
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-29.3020.950.960.94634454180
4.5-7.10.920.930.8718711560311
3.6-4.50.890.90.8523142029285
3.1-3.60.810.810.7523102063247
2.7-3.10.640.650.5440853707378
2.5-2.70.480.490.4125192304215

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.02phasing
RESOLVE2.02phasing
REFMAC5.1.19refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.01 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.237
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.227 687 5 %RANDOM
Rwork0.195 ---
all0.197 ---
obs0.197 13046 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2---0.27 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 32 48 2185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222174
X-RAY DIFFRACTIONr_angle_refined_deg1.881.9682950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.3495266
X-RAY DIFFRACTIONr_chiral_restr0.1250.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.021582
X-RAY DIFFRACTIONr_nbd_refined0.2350.2871
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4680.25
X-RAY DIFFRACTIONr_mcbond_it3.28521349
X-RAY DIFFRACTIONr_mcangle_it5.6742202
X-RAY DIFFRACTIONr_scbond_it7.7464825
X-RAY DIFFRACTIONr_scangle_it10.7846748
LS refinement shellResolution: 2.5→2.634 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.304 106
Rwork0.203 1870
Refinement TLS params.Method: refined / Origin x: 70.1423 Å / Origin y: 25.0227 Å / Origin z: 24.8646 Å
111213212223313233
T0.0515 Å20.0273 Å20.0151 Å2-0.0738 Å2-0.0211 Å2--0.0187 Å2
L3.2973 °22.6233 °2-0.2691 °2-4.7507 °2-0.5573 °2--1.482 °2
S-0.1542 Å °0.1009 Å °0.0496 Å °-0.091 Å °0.2226 Å °0.2762 Å °0.0485 Å °-0.0723 Å °-0.0684 Å °

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