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- PDB-5y27: Crystal structure of Se-Met Dpb4-Dpb3 -

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Basic information

Entry
Database: PDB / ID: 5y27
TitleCrystal structure of Se-Met Dpb4-Dpb3
Components
  • DNA polymerase epsilon subunit D
  • Putative transcription factor C16C4.22
KeywordsDNA BINDING PROTEIN / heterodimer / histone fold complex / DNA binging / 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 / DNA replication-dependent chromatin assembly / mitotic DNA replication initiation / leading strand elongation / nuclear replication fork / nucleosome binding / chromatin DNA binding / DNA-templated DNA replication / heterochromatin formation / 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 / SAD / Resolution: 1.9 Å
AuthorsLi, Y. / Gao, F. / Su, M. / Zhang, F.B. / Chen, Y.H.
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 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)38,1863
Polymers38,0942
Non-polymers921
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-48 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.291, 86.291, 59.710
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: 27506.492 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: 10587.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission 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.: 220 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.12 %
Preparation: The Solvent content/Matthews coefficient are the deposited values. Because the residues of A 107-240 had been degraded in the crystal.
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: 0.97915 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: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 20156 / % possible obs: 100 % / Redundancy: 49.9 % / Net I/σ(I): 72
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 50 % / Rmerge(I) obs: 0.713 / Num. unique obs: 2032 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→37.365 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.92
RfactorNum. reflection% reflection
Rfree0.2438 974 4.86 %
Rwork0.1918 --
obs0.1943 20047 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 0 6 220 1735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081549
X-RAY DIFFRACTIONf_angle_d1.0082084
X-RAY DIFFRACTIONf_dihedral_angle_d15.128606
X-RAY DIFFRACTIONf_chiral_restr0.044246
X-RAY DIFFRACTIONf_plane_restr0.005262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-2.00040.28861580.2372690X-RAY DIFFRACTION99
2.0004-2.12580.26821490.21722705X-RAY DIFFRACTION100
2.1258-2.28990.261080.20122739X-RAY DIFFRACTION100
2.2899-2.52030.23141360.20712711X-RAY DIFFRACTION100
2.5203-2.88480.24741640.22701X-RAY DIFFRACTION100
2.8848-3.63410.25011330.18562745X-RAY DIFFRACTION100
3.6341-37.37230.21551260.16422782X-RAY DIFFRACTION100
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)
12.5221-0.16991.08061.0368-0.18251.08960.0256-0.2111-0.03420.0422-0.00060.04460.0263-0.1662-0.01590.05080.0363-0.01270.21510.04440.072612.866735.564538.8838
21.3577-0.00470.75320.7424-0.17751.37150.10440.139-0.1877-0.10920.04870.16910.1327-0.069-0.14450.06550.0705-0.04770.22190.01550.13139.231931.899634.7505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 9:106)
2X-RAY DIFFRACTION2(chain B and resseq -4:87)

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