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- PDB-6zyc: Solution structure of the C-terminal domain of the vaccinia virus... -

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Basic information

Entry
Database: PDB / ID: 6zyc
TitleSolution structure of the C-terminal domain of the vaccinia virus DNA polymerase processivity factor component A20.
ComponentsDNA polymerase processivity factor component A20
KeywordsREPLICATION / Poxviridae / DNA polymerase holoenzyme / processivity factor binding
Function / homologyChordopoxvirus A20R / Chordopoxvirus A20R protein / viral DNA genome replication / DNA replication / DNA polymerase processivity factor component OPG148
Function and homology information
Biological speciesVaccinia virus
MethodSOLUTION NMR / molecular dynamics
AuthorsBersch, B. / Iseni, F. / Burmeister, W. / Tarbouriech, N.
Citation
Journal: J.Mol.Biol. / Year: 2021
Title: Solution Structure of the C-terminal Domain of A20, the Missing Brick for the Characterization of the Interface between Vaccinia Virus DNA Polymerase and its Processivity Factor.
Authors: Bersch, B. / Tarbouriech, N. / Burmeister, W.P. / Iseni, F.
#1: Journal: Nature Communications / Year: 2017
Title: The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding.
Authors: Tarbouriech, N. / Ducournau, C. / Hutin, S. / Mas, P.J. / Man, P. / Forest, E. / Hart, D.J. / Peyrefitte, C.N. / Burmeister, W. / Iseni, F.
History
DepositionJul 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase processivity factor component A20


Theoretical massNumber of molelcules
Total (without water)16,6691
Polymers16,6691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8580 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA polymerase processivity factor component A20


Mass: 16668.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 2-124 of the construct correspond to A20:304-426, residues 125-134 to a flexible linker and residues 136-148 to a Biotin Affinity Peptide (BAP),Residues 2-124 of the construct ...Details: Residues 2-124 of the construct correspond to A20:304-426, residues 125-134 to a flexible linker and residues 136-148 to a Biotin Affinity Peptide (BAP),Residues 2-124 of the construct correspond to A20:304-426, residues 125-134 to a flexible linker and residues 136-148 to a Biotin Affinity Peptide (BAP)
Source: (gene. exp.) Vaccinia virus (strain Copenhagen) / Strain: Copenhagen / Gene: A20R / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Star / References: UniProt: P20995

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 15N-TROSY
123isotropic12D 13C-HSQC
134isotropic33D HNCO
144isotropic13D HN(CA)CB
153isotropic23D (H)CCH-TOCSY
181isotropic115N-NOESY
173isotropic113C-NOESY
162isotropic12D-NOESY
193isotropic113C-13C-methyl-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-15N] A20-BAP, 50 mM sodium citrate, 300 mM sodium chloride, 2 mg/L TCEP, 90% H2O/10% D2O15N-A20-BAP90% H2O/10% D2O
solution41 mM [U-15N] A20-BAP, 50 mM sodium citrate, 300 mM sodium chloride, 2 mg/L TCEP, 90% H2O/10% D2O15N13C-A20-BAP-initial90% H2O/10% D2O
solution21 mM [U-15N] A20-BAP, 50 mM potassium phosphate, 300 mM sodium chloride, 1.2 mM TCEP, 100% D2O15N-A20-BAP-D2O100% D2O
solution31 mM [U-15N] A20-BAP, 50 mM potassium phosphate, 300 mM sodium chloride, 1.2 mM TCEP, 90% H2O/10% D2O13C15N-A20-BAP90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMA20-BAP[U-15N]1
50 mMsodium citratenatural abundance1
300 mMsodium chloridenatural abundance1
2 mg/LTCEPnatural abundance1
1 mMA20-BAP[U-15N]4
50 mMsodium citratenatural abundance4
300 mMsodium chloridenatural abundance4
2 mg/LTCEPnatural abundance4
1 mMA20-BAP[U-15N]2
50 mMpotassium phosphatenatural abundance2
300 mMsodium chloridenatural abundance2
1.2 mMTCEPnatural abundance2
1 mMA20-BAP[U-15N]3
50 mMpotassium phosphatenatural abundance3
300 mMsodium chloridenatural abundance3
1.2 mMTCEPnatural abundance3
Sample conditionsIonic strength: 0.3 M / Label: general / pH: 6 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9501
Bruker AVANCEBrukerAVANCE8502
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
UNIOTorsten Herrmannpeak picking
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 5 / Details: water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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