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- PDB-7e15: Protein ternary complex working for DNA replication initiation -

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Basic information

Entry
Database: PDB / ID: 7.0E+15
TitleProtein ternary complex working for DNA replication initiation
Components
  • DNA polymerase II small subunit
  • Gins51
  • SsDNA-specific exonuclease
KeywordsDNA BINDING PROTEIN/REPLICATION / DNA replication / DNA BINDING PROTEIN-REPLICATION COMPLEX / REPLICATION
Function / homology
Function and homology information


exodeoxyribonuclease I / single-stranded DNA 5'-3' DNA exonuclease activity / DNA polymerase complex / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / DNA strand elongation involved in DNA replication / DNA recombination / DNA-directed DNA polymerase / nucleic acid binding / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Archaeal GINS complex, Gins51 subunit / : / Gins51, C-terminal domain / : / DHH-CID domain / DNA polymerase II small subunit, archaeal / : / DNA polymerase II small subunit, N-terminal domain / inorganic pyrophosphatase (n-terminal core) - #30 / : ...Archaeal GINS complex, Gins51 subunit / : / Gins51, C-terminal domain / : / DHH-CID domain / DNA polymerase II small subunit, archaeal / : / DNA polymerase II small subunit, N-terminal domain / inorganic pyrophosphatase (n-terminal core) - #30 / : / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / DNA polymerase delta/II small subunit family / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Metallo-dependent phosphatase-like / Nucleic acid-binding, OB-fold / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA polymerase II small subunit / Gins51 C-terminal domain-containing protein / Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsOyama, T. / Ishino, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06081 Japan
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome.
Authors: Oki, K. / Nagata, M. / Yamagami, T. / Numata, T. / Ishino, S. / Oyama, T. / Ishino, Y.
History
DepositionJan 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 11, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SsDNA-specific exonuclease
B: Gins51
C: DNA polymerase II small subunit
D: SsDNA-specific exonuclease
E: Gins51
F: DNA polymerase II small subunit


Theoretical massNumber of molelcules
Total (without water)138,3406
Polymers138,3406
Non-polymers00
Water1,62190
1
A: SsDNA-specific exonuclease
B: Gins51
C: DNA polymerase II small subunit


Theoretical massNumber of molelcules
Total (without water)69,1703
Polymers69,1703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-20 kcal/mol
Surface area24230 Å2
MethodPISA
2
D: SsDNA-specific exonuclease
E: Gins51
F: DNA polymerase II small subunit


Theoretical massNumber of molelcules
Total (without water)69,1703
Polymers69,1703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-20 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.302, 48.308, 205.759
Angle α, β, γ (deg.)90.000, 96.195, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein SsDNA-specific exonuclease


Mass: 52910.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1252 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5JGL0
#2: Protein Gins51


Mass: 9008.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0536 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5JF31
#3: Protein DNA polymerase II small subunit / PolDP1 / Pol II / Exodeoxyribonuclease small subunit


Mass: 7251.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: polB, TK1902 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5JET1, DNA-directed DNA polymerase, exodeoxyribonuclease I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.15 M DL-malic acid (pH 7.0), 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 29, 2017 / Details: two dimensional focusing mirror
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 93014 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 31.22 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.077 / Rrim(I) all: 0.11 / Net I/σ(I): 6.9
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2 / Num. unique obs: 16322 / CC1/2: 0.927 / Rpim(I) all: 0.395 / Rrim(I) all: 0.56 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ghr

5ghr


Resolution: 2.45→47.01 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 30.6113
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2419 4386 4.72 %
Rwork0.2162 88628 -
obs0.2174 93014 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.54 Å2
Refinement stepCycle: LAST / Resolution: 2.45→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8884 0 0 90 8974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029034
X-RAY DIFFRACTIONf_angle_d0.476812205
X-RAY DIFFRACTIONf_chiral_restr0.04051380
X-RAY DIFFRACTIONf_plane_restr0.00281595
X-RAY DIFFRACTIONf_dihedral_angle_d14.18733341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.3721660.34123047X-RAY DIFFRACTION95.57
2.48-2.510.36851570.3242842X-RAY DIFFRACTION95.03
2.51-2.540.3171720.31353016X-RAY DIFFRACTION94.94
2.54-2.570.30931550.30712993X-RAY DIFFRACTION96.45
2.57-2.60.28371600.29332855X-RAY DIFFRACTION96.42
2.6-2.640.30521810.29623012X-RAY DIFFRACTION95.66
2.64-2.680.30761790.29712887X-RAY DIFFRACTION94.51
2.68-2.720.32381550.28462966X-RAY DIFFRACTION96.87
2.72-2.760.33591420.29222989X-RAY DIFFRACTION96.73
2.76-2.80.32921510.27612962X-RAY DIFFRACTION95.61
2.8-2.850.29351580.28092923X-RAY DIFFRACTION95.12
2.85-2.90.36191490.2693043X-RAY DIFFRACTION97.23
2.9-2.960.29971510.25352907X-RAY DIFFRACTION95.65
2.96-3.020.34581020.25893100X-RAY DIFFRACTION94.68
3.02-3.090.26531370.25232847X-RAY DIFFRACTION96.29
3.09-3.160.27851530.23693005X-RAY DIFFRACTION96.19
3.16-3.240.28761360.23982981X-RAY DIFFRACTION94.43
3.24-3.320.26131270.24772931X-RAY DIFFRACTION95.98
3.33-3.420.2441120.2353036X-RAY DIFFRACTION95.6
3.42-3.530.27561500.20232933X-RAY DIFFRACTION95.21
3.53-3.660.23381570.20192962X-RAY DIFFRACTION94.43
3.66-3.810.21581400.19512891X-RAY DIFFRACTION94.34
3.81-3.980.15621580.17952877X-RAY DIFFRACTION93.38
3.98-4.190.15171250.162869X-RAY DIFFRACTION92.32
4.19-4.450.15511340.15612967X-RAY DIFFRACTION94.34
4.45-4.790.1851530.14762864X-RAY DIFFRACTION93.49
4.79-5.280.20171480.17162978X-RAY DIFFRACTION95.65
5.28-6.040.2021150.18323027X-RAY DIFFRACTION96.17
6.04-7.60.18151100.18082988X-RAY DIFFRACTION96.36
7.6-47.010.18581530.14282930X-RAY DIFFRACTION94.92

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