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- PDB-5y26: Crystal structure of native Dpb4-Dpb3 -

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Basic information

Entry
Database: PDB / ID: 5y26
TitleCrystal structure of native Dpb4-Dpb3
Components
  • DNA polymerase epsilon subunit D
  • Putative transcription factor C16C4.22
KeywordsDNA BINDING PROTEIN / Heterodimer / Histone fold complex / DNA binding / Epigenetic
Function / homology
Function and homology information


CMG complex assembly / DNA replication initiation / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER ...CMG complex assembly / DNA replication initiation / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / epsilon DNA polymerase complex / DNA strand elongation involved in mitotic DNA replication / mitotic DNA replication initiation / leading strand elongation / nuclear replication fork / heterochromatin formation / DNA-templated DNA replication / chromatin DNA binding / protein heterodimerization activity / DNA damage response / chromatin / nucleus / cytosol
Similarity search - Function
Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / Histone, subunit A / Histone, subunit A / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA polymerase epsilon subunit C / DNA polymerase epsilon subunit D
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsChen, Y.H. / Li, Y. / Gao, F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Coordinated regulation of heterochromatin inheritance by Dpb3-Dpb4 complex.
Authors: He, H. / Li, Y. / Dong, Q. / Chang, A.Y. / Gao, F. / Chi, Z. / Su, M. / Zhang, F. / Ban, H. / Martienssen, R. / Chen, Y.H. / Li, F.
History
DepositionJul 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

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Assembly

Deposited unit
A: DNA polymerase epsilon subunit D
B: Putative transcription factor C16C4.22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9513
Polymers37,8592
Non-polymers921
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-48 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.517, 86.517, 59.799
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein DNA polymerase epsilon subunit D / DNA polymerase II subunit D


Mass: 27318.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: dpb4, SPBC3D6.09
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: P87174, DNA-directed DNA polymerase
#2: Protein Putative transcription factor C16C4.22 / Dpb3


Mass: 10540.134 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: SPCC16C4.22
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: C6Y4D0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1.71 Å3/Da / Density % sol: 27.92 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: PEG 3350, ches

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16922 / % possible obs: 97.8 % / Redundancy: 15.1 % / Net I/σ(I): 27
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.661 / Num. unique obs: 1708 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.003→43.258 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.77
RfactorNum. reflection% reflection
Rfree0.2244 790 4.75 %
Rwork0.1808 --
obs0.1828 16635 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.003→43.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 6 138 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081554
X-RAY DIFFRACTIONf_angle_d0.9732093
X-RAY DIFFRACTIONf_dihedral_angle_d15.411607
X-RAY DIFFRACTIONf_chiral_restr0.039247
X-RAY DIFFRACTIONf_plane_restr0.004264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0025-2.1280.27731400.23652574X-RAY DIFFRACTION95
2.128-2.29230.2845940.2282417X-RAY DIFFRACTION88
2.2923-2.52290.23661540.20652702X-RAY DIFFRACTION100
2.5229-2.8880.2371450.19192727X-RAY DIFFRACTION100
2.888-3.63820.22421380.17492738X-RAY DIFFRACTION100
3.6382-43.26860.18661190.14872687X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -11.2517 Å / Origin y: 33.9877 Å / Origin z: 0.287 Å
111213212223313233
T0.1139 Å2-0.0296 Å2-0.0074 Å2-0.2977 Å2-0.0386 Å2--0.1892 Å2
L2.8246 °20.6052 °21.2661 °2-1.9078 °20.6686 °2--3.741 °2
S0.179 Å °0.041 Å °-0.209 Å °0.0415 Å °-0.0114 Å °-0.0557 Å °0.2327 Å °0.1901 Å °-0.1448 Å °
Refinement TLS groupSelection details: all

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