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- PDB-8f69: Crystal structure of murine PolG2 dimer bound to DNA -

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Basic information

Entry
Database: PDB / ID: 8f69
TitleCrystal structure of murine PolG2 dimer bound to DNA
Components
  • DNA (5'-D(*CP*TP*GP*GP*TP*AP*GP*GP*CP*GP*CP*CP*TP*AP*CP*CP*AP*G)-3')
  • DNA polymerase subunit gamma-2, mitochondrial
KeywordsDNA BINDING PROTEIN/DNA / DNA Complex / PolG accessory subunit / mitochondria / mtDNA / processivity factor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


mitochondrial DNA replication / mitochondrial nucleoid / DNA binding
Similarity search - Function
Glycyl-tRNA synthetase-like core domain / POLG2, C-terminal / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase subunit gamma-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWojtaszek, J.L. / Hoff, K.E. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structure-specific roles for PolG2-DNA complexes in maintenance and replication of mitochondrial DNA.
Authors: Wojtaszek, J.L. / Hoff, K.E. / Longley, M.J. / Kaur, P. / Andres, S.N. / Wang, H. / Williams, R.S. / Copeland, W.C.
History
DepositionNov 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA polymerase subunit gamma-2, mitochondrial
A: DNA polymerase subunit gamma-2, mitochondrial
C: DNA (5'-D(*CP*TP*GP*GP*TP*AP*GP*GP*CP*GP*CP*CP*TP*AP*CP*CP*AP*G)-3')
D: DNA (5'-D(*CP*TP*GP*GP*TP*AP*GP*GP*CP*GP*CP*CP*TP*AP*CP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,79521
Polymers107,4954
Non-polymers1,30117
Water2,324129
1
B: DNA polymerase subunit gamma-2, mitochondrial
A: DNA polymerase subunit gamma-2, mitochondrial
hetero molecules

C: DNA (5'-D(*CP*TP*GP*GP*TP*AP*GP*GP*CP*GP*CP*CP*TP*AP*CP*CP*AP*G)-3')
D: DNA (5'-D(*CP*TP*GP*GP*TP*AP*GP*GP*CP*GP*CP*CP*TP*AP*CP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)108,79521
Polymers107,4954
Non-polymers1,30117
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444y-1/2,-x-1/2,z-1/41
Buried area13480 Å2
ΔGint-38 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.027, 88.027, 343.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein / DNA chain , 2 types, 4 molecules BACD

#1: Protein DNA polymerase subunit gamma-2, mitochondrial


Mass: 48229.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Polg2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0VES3
#2: DNA chain DNA (5'-D(*CP*TP*GP*GP*TP*AP*GP*GP*CP*GP*CP*CP*TP*AP*CP*CP*AP*G)-3')


Mass: 5517.567 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 146 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% MPD 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→42.63 Å / Num. obs: 69448 / % possible obs: 99.69 % / Redundancy: 8.9 % / Biso Wilson estimate: 59.36 Å2 / Rrim(I) all: 0.127 / Net I/σ(I): 20.59
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6754 / Rrim(I) all: 1.49 / % possible all: 99.16

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G5I

1g5i


Resolution: 2.2→42.63 Å / SU ML: 0.3068 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2283 1998 2.88 %
Rwork0.1939 67401 -
obs0.1949 69399 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.91 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6377 732 84 129 7322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00437447
X-RAY DIFFRACTIONf_angle_d0.632710240
X-RAY DIFFRACTIONf_chiral_restr0.04111152
X-RAY DIFFRACTIONf_plane_restr0.0041173
X-RAY DIFFRACTIONf_dihedral_angle_d18.18424301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.35371370.34234692X-RAY DIFFRACTION98.65
2.26-2.320.31321410.29284719X-RAY DIFFRACTION99.98
2.32-2.390.3111390.26624733X-RAY DIFFRACTION99.96
2.39-2.460.28351410.23974734X-RAY DIFFRACTION99.92
2.46-2.550.29981410.23054755X-RAY DIFFRACTION100
2.55-2.650.30691420.22234779X-RAY DIFFRACTION99.98
2.65-2.770.26241420.21214769X-RAY DIFFRACTION99.96
2.77-2.920.24851410.20894790X-RAY DIFFRACTION100
2.92-3.10.26791430.21854791X-RAY DIFFRACTION99.96
3.1-3.340.28891430.21014820X-RAY DIFFRACTION99.92
3.34-3.680.24041430.19484866X-RAY DIFFRACTION100
3.68-4.210.22851450.17614881X-RAY DIFFRACTION99.96
4.21-5.30.16831460.15544888X-RAY DIFFRACTION98.9
5.3-42.630.19851540.1885184X-RAY DIFFRACTION98.74
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)
14.16552155796-0.517510043817-0.6181106024661.996643333390.7895072093870.910027438035-0.4179955203340.1350798540430.2118572765940.0550065835996-0.0323714269687-0.203049160372-0.1116177765950.0177471231450.4150816409090.648628248488-0.010336960073-0.1120019575590.3782935787250.03846598106780.774339965116-23.05431708133.59646029141-39.6906685802
21.815824214720.01142084999320.05248082611682.785480353251.101902289314.24300248138-0.2434258168750.1716484807460.425353657708-0.5218384772790.001355783253910.064293524025-1.232233174350.1126371083020.2145595942860.7922006078750.0155999676911-0.2010275798510.4013332875810.007632681138160.707492495823-35.438847062313.4642151145-47.6346339137
37.028856152922.62523904210.3283246147995.19047104239-2.276500027277.02230461328-0.534370802745-0.276830121815-0.6351445151920.5103376979750.1611459746350.5601010719990.231482045904-0.9754691342760.4068414058440.6838880174880.1814677207720.1924100178520.837959026565-0.2519156506560.997846880908-57.2156203674-2.30480593493-21.2942895962
44.805048936080.3992054891780.06684947831171.279974445560.2851432039380.506028924105-0.117469377349-0.02365354787330.20620677383-0.04082705047420.0187854543479-0.267890340893-0.1681015119430.1285340123650.08128260434870.558079524720.03713680644550.04541022851190.3694317210450.02006515653390.644855893258-23.2053562738-5.77538650373-45.2012491222
52.36954189695-0.4295034575360.7785124766942.17963620906-0.02076201107994.45955654172-0.0333762424808-0.192059971771-0.04592295020810.250164056610.0435244888537-0.07440413294330.1596456265750.258963933142-0.01151561442840.4261072592850.05484079558860.01041569735690.321055661827-0.02950312274780.427502436804-32.3175648486-18.0840496061-33.5678641015
67.68134565577-2.10085648560.9736971517225.62116940388-1.566091148873.526131739690.08356477019920.4519975135590.094796618561-0.5685909761160.01812913592550.2662771972670.008236523608720.113419078542-0.04191346967040.471602377701-0.0929512879695-0.04581508521380.368554008128-0.05744113140120.359918148475-56.9148185808-6.67049916132-61.6083227421
72.07926696094-0.30927287191.367099249726.40723969182-5.018440289964.595238545981.0037608591.24404018865-0.986379998416-0.252254968173-1.004333390351.74980803386-1.0966771456-0.517558168221-0.2343453880011.43622843470.885275517014-0.3225977091781.60002011831-0.4771020449231.30278869081-64.1640536121-0.0496640152166-0.394846701651
89.31062256122-1.683934523560.1460335883752.762007510930.5160377795156.29018596015-1.202954925140.330943540351-0.7086049802270.5764610912440.274260998627-0.5610491631271.080766710120.820544376720.8966103493040.9544131385750.182485498518-0.05716957529720.979160095427-0.05921141245771.03569829708-42.2655981215-20.24645164121.90046715257
93.09113127446-1.011119190873.090912216452.48361415302-2.098534039033.63836717743-0.166903169595-1.60166332238-1.296744837391.96648548456-0.4825255660820.8263758091670.822649588230.7164763038550.726728451981.228009034220.3701020623350.06511199454291.24608457180.1613459101730.908926313623-36.8131682048-19.64603716086.99723205962
105.76469137296-2.74829897169-0.249949916075.24014499629-0.4693552067080.963902942197-0.07603883195560.6884902062330.2822744159260.24697884025-0.5669171180450.26674897214-1.08021590951-1.205419183120.5234572670331.012792917810.47229508823-0.1603699194111.52113959709-0.07916780911741.07037619785-60.3334405025-2.98767285409-0.413507472563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 41 through 151 )
2X-RAY DIFFRACTION2chain 'B' and (resid 152 through 356 )
3X-RAY DIFFRACTION3chain 'B' and (resid 357 through 458 )
4X-RAY DIFFRACTION4chain 'A' and (resid 38 through 159 )
5X-RAY DIFFRACTION5chain 'A' and (resid 160 through 330 )
6X-RAY DIFFRACTION6chain 'A' and (resid 331 through 459 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 10 )
8X-RAY DIFFRACTION8chain 'C' and (resid 11 through 18 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 5 )
10X-RAY DIFFRACTION10chain 'D' and (resid 6 through 18 )

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