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- PDB-5zkj: Human EXOG-H140A in complex with RNA/DNA hybrid duplex -

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Basic information

Entry
Database: PDB / ID: 5zkj
TitleHuman EXOG-H140A in complex with RNA/DNA hybrid duplex
Components
  • DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3')
  • Nuclease EXOG, mitochondrial
  • RNA (5'-R(P*CP*GP*GP*GP*AP*UP*GP*UP*CP*AP*CP*G)-3')
KeywordsHYDROLASE/RNA/DNA / Enzyme-substrate complex / Mitochondrial exonuclease / HYDROLASE-RNA-DNA complex
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / Strand-asynchronous mitochondrial DNA replication / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / mitochondrial matrix ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / Strand-asynchronous mitochondrial DNA replication / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / mitochondrial matrix / protein-containing complex / mitochondrion / metal ion binding / nucleus
Similarity search - Function
EXOG, C-terminal / Endo/exonuclease (EXOG) C-terminal domain / 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
DNA / DNA (> 10) / RNA / RNA (> 10) / Nuclease EXOG, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 Å
AuthorsWu, C.C. / Lin, J.L.J. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication.
Authors: Wu, C.C. / Lin, J.L.J. / Yang-Yen, H.F. / Yuan, H.S.
History
DepositionMar 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclease EXOG, mitochondrial
B: Nuclease EXOG, mitochondrial
C: RNA (5'-R(P*CP*GP*GP*GP*AP*UP*GP*UP*CP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3')
E: RNA (5'-R(P*CP*GP*GP*GP*AP*UP*GP*UP*CP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4989
Polymers93,4146
Non-polymers843
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-122 kcal/mol
Surface area32830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.576, 167.576, 105.438
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein / RNA chain / DNA chain , 3 types, 6 molecules ABCEDF

#1: Protein Nuclease EXOG, mitochondrial / Endonuclease G-like 1 / Endo G-like 1


Mass: 39216.262 Da / Num. of mol.: 2 / Mutation: H140A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOG, ENDOGL1, ENDOGL2, ENGL / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS
References: UniProt: Q9Y2C4, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters
#2: RNA chain RNA (5'-R(P*CP*GP*GP*GP*AP*UP*GP*UP*CP*AP*CP*G)-3')


Mass: 3867.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3')


Mass: 3623.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 53 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0, 22% PEG 400

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 20, 2017
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.798→30 Å / Num. obs: 25994 / % possible obs: 95.8 % / Redundancy: 1.9 % / CC1/2: 0.934 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.044 / Rrim(I) all: 0.066 / Χ2: 1.003 / Net I/σ(I): 13.6
Reflection shellResolution: 2.798→2.88 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.747 / Num. unique obs: 2202 / CC1/2: 0.706 / Rpim(I) all: 0.435 / Rrim(I) all: 0.64 / Χ2: 0.999 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T4I

5t4i


Resolution: 2.798→28.434 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1340 5.16 %Random selection
Rwork0.1806 ---
obs0.1831 25986 95.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.798→28.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 1000 3 50 5860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036059
X-RAY DIFFRACTIONf_angle_d0.4878419
X-RAY DIFFRACTIONf_dihedral_angle_d13.773523
X-RAY DIFFRACTIONf_chiral_restr0.04935
X-RAY DIFFRACTIONf_plane_restr0.003921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7978-2.89770.32741490.28942404X-RAY DIFFRACTION94
2.8977-3.01360.30991260.26352550X-RAY DIFFRACTION98
3.0136-3.15060.32511310.23632572X-RAY DIFFRACTION99
3.1506-3.31650.29281290.22412550X-RAY DIFFRACTION98
3.3165-3.52390.24211140.20882520X-RAY DIFFRACTION97
3.5239-3.79540.23531190.19272518X-RAY DIFFRACTION97
3.7954-4.17630.23841870.17162397X-RAY DIFFRACTION95
4.1763-4.77820.21231340.14972409X-RAY DIFFRACTION93
4.7782-6.01060.21421290.15662415X-RAY DIFFRACTION93
6.0106-28.43530.17141220.15842311X-RAY DIFFRACTION89

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