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- PDB-9m0g: Crystal structure of human endonuclease G mutant C113A/H141A boun... -

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Basic information

Entry
Database: PDB / ID: 9m0g
TitleCrystal structure of human endonuclease G mutant C113A/H141A bound with trans-Resveratrol
ComponentsEndonuclease G, mitochondrial
KeywordsAPOPTOSIS / His-Me finger endonucleases
Function / homology
Function and homology information


mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / positive regulation of mitochondrial DNA replication / positive regulation of apoptotic DNA fragmentation / single-stranded DNA endonuclease activity / apoptotic DNA fragmentation / negative regulation of TOR signaling / response to tumor necrosis factor / response to mechanical stimulus ...mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / positive regulation of mitochondrial DNA replication / positive regulation of apoptotic DNA fragmentation / single-stranded DNA endonuclease activity / apoptotic DNA fragmentation / negative regulation of TOR signaling / response to tumor necrosis factor / response to mechanical stimulus / RNA endonuclease activity / positive regulation of autophagy / cellular response to calcium ion / DNA endonuclease activity / cellular response to glucose stimulus / response to estradiol / cellular response to oxidative stress / DNA recombination / cellular response to hypoxia / in utero embryonic development / nucleic acid binding / perikaryon / mitochondrial inner membrane / positive regulation of apoptotic process / response to antibiotic / DNA damage response / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / mitochondrion / nucleus
Similarity search - Function
DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily
Similarity search - Domain/homology
5-[2-(4-hydroxyphenyl)ethyl]benzene-1,3-diol / Endonuclease G, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsYang, W.Z. / Yuan, H.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal structure of human endonuclease G mutant C113A/H141A bound with trans-Resveratrol
Authors: Yang, W.Z. / Yuan, H.S.
History
DepositionFeb 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease G, mitochondrial
B: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6695
Polymers67,3912
Non-polymers2793
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-44 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.305, 70.561, 88.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endonuclease G, mitochondrial / Endo G


Mass: 33695.270 Da / Num. of mol.: 2 / Mutation: C113A,H141A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENDOG / Production host: Escherichia coli (E. coli)
References: UniProt: Q14249, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RE2 / 5-[2-(4-hydroxyphenyl)ethyl]benzene-1,3-diol / Dihydroresveratrol


Mass: 230.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 1.5 Å3/Da / Density % sol: 17.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.02 M Citric acid, 0.08 M BIS-TRIS propane / pH 8.0, 16% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 3.19→30 Å / Num. obs: 7033 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.181 / Χ2: 0.157 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.2-3.266.80.5043301.0371100
3.26-3.3170.4993431.081199.7
3.31-3.3870.4423461.0141100
3.38-3.457.10.4263451.0671100
3.45-3.527.20.3533511.0791100
3.52-3.67.10.3333421.0171100
3.6-3.697.10.2753431.076199.7
3.69-3.797.20.2723520.9981100
3.79-3.970.2353431.0091100
3.9-4.037.10.2133510.976199.4
4.03-4.1770.1683420.9621100
4.17-4.346.90.163591.0171100
4.34-4.546.70.1283410.8931100
4.54-4.786.70.1213540.932199.7
4.78-5.076.80.1153490.831199.4
5.07-5.466.80.1083590.7571100
5.46-6.016.90.1083550.735199.7
6.01-6.876.80.1023700.696199.7
6.87-8.626.50.0943680.749199.7
8-105.50.1183901.271196.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NJT

6njt


Resolution: 3.2→29.26 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3006 671 10 %
Rwork0.1976 --
obs0.2079 6710 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 0 19 0 3598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015
X-RAY DIFFRACTIONf_angle_d1.6
X-RAY DIFFRACTIONf_dihedral_angle_d8.539513
X-RAY DIFFRACTIONf_chiral_restr0.067529
X-RAY DIFFRACTIONf_plane_restr0.013662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.440.36011140.22241020X-RAY DIFFRACTION83
3.44-3.780.31171330.21751202X-RAY DIFFRACTION96
3.78-4.330.32731380.19021251X-RAY DIFFRACTION100
4.33-5.440.26351400.17491254X-RAY DIFFRACTION99
5.45-100.29061460.20441312X-RAY DIFFRACTION98

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