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- PDB-6iid: Human EXOG-H140A in complex with RNA-DNA chimeric duplex -

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Basic information

Entry
Database: PDB / ID: 6iid
TitleHuman EXOG-H140A in complex with RNA-DNA chimeric duplex
Components
  • DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3')
  • DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)-R(P*CP*AP*CP*G)-3')
  • Nuclease EXOG, mitochondrial
KeywordsHYDROLASE/DNA / Enzyme-substrate complex / Mitochondrial exonuclease / HYDROLASE-DNA complex / DNA BINDING PROTEIN
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) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Nuclease EXOG, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.986 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
DepositionOct 4, 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 1.4Nov 6, 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: Nuclease EXOG, mitochondrial
D: Nuclease EXOG, mitochondrial
E: DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)-R(P*CP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3')
G: DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)-R(P*CP*AP*CP*G)-3')
H: DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3')
I: DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)-R(P*CP*AP*CP*G)-3')
J: DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3')
K: DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)-R(P*CP*AP*CP*G)-3')
L: 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)186,39716
Polymers186,30012
Non-polymers974
Water79344
1
A: Nuclease EXOG, mitochondrial
B: Nuclease EXOG, mitochondrial
E: DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)-R(P*CP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3')
G: DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)-R(P*CP*AP*CP*G)-3')
H: 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)93,1998
Polymers93,1506
Non-polymers492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nuclease EXOG, mitochondrial
D: Nuclease EXOG, mitochondrial
I: DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)-R(P*CP*AP*CP*G)-3')
J: DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3')
K: DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)-R(P*CP*AP*CP*G)-3')
L: 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)93,1998
Polymers93,1506
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.710, 75.953, 81.152
Angle α, β, γ (deg.)72.96, 90.01, 70.75
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 39216.262 Da / Num. of mol.: 4 / 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: DNA/RNA hybrid
DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)-R(P*CP*AP*CP*G)-3') / R2-DNA


Mass: 3735.416 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium formate dehydrate and 20% [w/v] PEG 3350
PH range: 6.6-7.2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 3, 2018
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: 2.986→30 Å / Num. obs: 30771 / % possible obs: 96.7 % / Redundancy: 1.9 % / CC1/2: 0.941 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.085 / Rrim(I) all: 0.12 / Χ2: 0.999 / Net I/σ(I): 8.9
Reflection shellResolution: 3→3.08 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 2246 / CC1/2: 0.855 / Rpim(I) all: 0.432 / Rrim(I) all: 0.611 / Χ2: 1.008 / % possible all: 91.9

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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: 5ZKI

5zki


Resolution: 2.986→29.834 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.65
RfactorNum. reflection% reflection
Rfree0.2522 1562 5.08 %
Rwork0.1994 --
obs0.2021 30748 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.986→29.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9348 1346 4 44 10742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411098
X-RAY DIFFRACTIONf_angle_d0.50415266
X-RAY DIFFRACTIONf_dihedral_angle_d14.8616438
X-RAY DIFFRACTIONf_chiral_restr0.0421661
X-RAY DIFFRACTIONf_plane_restr0.0031754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9856-3.08180.33731130.27932314X-RAY DIFFRACTION83
3.0818-3.19190.32461410.26272598X-RAY DIFFRACTION93
3.1919-3.31950.29291330.23432617X-RAY DIFFRACTION94
3.3195-3.47040.27811390.22352619X-RAY DIFFRACTION95
3.4704-3.6530.24861330.20522693X-RAY DIFFRACTION97
3.653-3.88150.25261410.20492717X-RAY DIFFRACTION98
3.8815-4.18040.23951510.18442709X-RAY DIFFRACTION99
4.1804-4.59970.23241600.16612724X-RAY DIFFRACTION99
4.5997-5.26220.241600.16252743X-RAY DIFFRACTION99
5.2622-6.61780.24711320.20452735X-RAY DIFFRACTION99
6.6178-29.83530.23251590.19652717X-RAY DIFFRACTION99

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