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- PDB-5vbn: Crystal Structure of human DNA polymerase epsilon B-subunit in co... -

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Basic information

Entry
Database: PDB / ID: 5vbn
TitleCrystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit
Components
  • DNA polymerase epsilon catalytic subunit A
  • DNA polymerase epsilon subunit 2
KeywordsTRANSFERASE / replication / DNA replication / polymerase / DNA polymerase / DNA polymerase epsilon / B-subunit / catalytic subunit
Function / homology
Function and homology information


epsilon DNA polymerase complex / DNA replication initiation / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / leading strand elongation / DNA synthesis involved in DNA repair / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex ...epsilon DNA polymerase complex / DNA replication initiation / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / leading strand elongation / DNA synthesis involved in DNA repair / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / error-prone translesion synthesis / embryonic organ development / base-excision repair, gap-filling / Gap-filling DNA repair synthesis and ligation in GG-NER / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / G1/S transition of mitotic cell cycle / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / nucleotide binding / DNA repair / intracellular membrane-bounded organelle / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
DNA polymerase epsilon subunit B, N-terminal / DNA polymerases epsilon N terminal / DNA polymerase epsilon, subunit B / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / DNA polymerase family B, thumb domain ...DNA polymerase epsilon subunit B, N-terminal / DNA polymerases epsilon N terminal / DNA polymerase epsilon, subunit B / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / DNA polymerase family B, thumb domain / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional 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
DNA polymerase epsilon subunit 2 / DNA polymerase epsilon catalytic subunit A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsBaranovskiy, A.G. / Gu, J. / Suwa, Y. / Babayeva, N.D. / Tahirov, T.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM101167 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA036727 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Crystal structure of the human Pol B-subunit in complex with the C-terminal domain of the catalytic subunit.
Authors: Baranovskiy, A.G. / Gu, J. / Babayeva, N.D. / Kurinov, I. / Pavlov, Y.I. / Tahirov, T.H.
History
DepositionMar 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 10, 2018Group: Data collection / Refinement description / Structure summary
Category: entity / pdbx_xplor_file / refine / Item: _entity.formula_weight
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 epsilon subunit 2
B: DNA polymerase epsilon catalytic subunit A
E: DNA polymerase epsilon subunit 2
F: DNA polymerase epsilon catalytic subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,69010
Polymers152,2364
Non-polymers4546
Water3,819212
1
A: DNA polymerase epsilon subunit 2
B: DNA polymerase epsilon catalytic subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3455
Polymers76,1182
Non-polymers2273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-38 kcal/mol
Surface area23620 Å2
MethodPISA
2
E: DNA polymerase epsilon subunit 2
F: DNA polymerase epsilon catalytic subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3455
Polymers76,1182
Non-polymers2273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-39 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.260, 201.459, 78.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA polymerase epsilon subunit 2 / / DNA polymerase II subunit 2 / DNA polymerase epsilon subunit B


Mass: 59600.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLE2, DPE2 / Production host: Escherichia coli (E. coli) / References: UniProt: P56282, DNA-directed DNA polymerase
#2: Protein DNA polymerase epsilon catalytic subunit A / DNA polymerase II subunit A


Mass: 16517.137 Da / Num. of mol.: 2 / Fragment: UNP residues 2142-2286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLE, POLE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07864, DNA-directed DNA polymerase
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 50 mM sodium citrate, pH5.6, 0.70 M ammonium sulfate and 2 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 61804 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3044 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→39.75 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 3006919.42 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2958 5.1 %RANDOM
Rwork0.225 ---
obs0.225 58410 94.7 %-
Solvent computationBsol: 38.3459 Å2 / ksol: 0.373505 e/Å3
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.42 Å
Refinement stepCycle: 1 / Resolution: 2.35→39.75 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 464 5.1 %
Rwork0.329 8677 -
obs--90.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION3CNS_TOPPAR/ion.paramCNS_TOPPAR/iom.top

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