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- PDB-6j80: Human mitochondrial Oligoribonuclease in complex with poly-dT DNA -

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Basic information

Entry
Database: PDB / ID: 6j80
TitleHuman mitochondrial Oligoribonuclease in complex with poly-dT DNA
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
  • Oligoribonuclease, mitochondrialOligonucleotidase
KeywordsHYDROLASE/DNA / Exoribonuclease / Mitochonrial Oligoribonuclease / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


Mitochondrial RNA degradation / Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix ...Mitochondrial RNA degradation / Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix / focal adhesion / nucleolus / magnesium ion binding / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Oligoribonuclease / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
CITRIC ACID / DNA / Oligoribonuclease, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.812 Å
AuthorsChu, L.Y. / Agrawal, S. / Yuan, H.S.
CitationJournal: Rna / Year: 2019
Title: Structural insights into nanoRNA degradation by human Rexo2.
Authors: Chu, L.Y. / Agrawal, S. / Chen, Y.P. / Yang, W.Z. / Yuan, H.S.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oligoribonuclease, mitochondrial
B: Oligoribonuclease, mitochondrial
C: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2296
Polymers43,9893
Non-polymers2413
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-38 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.079, 88.403, 45.939
Angle α, β, γ (deg.)90.000, 105.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Oligoribonuclease, mitochondrial / Oligonucleotidase


Mass: 20952.057 Da / Num. of mol.: 2 / Mutation: D199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y3B8
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2084.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.9 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium citrate dibasic, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 45376 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.75 Å2 / Rmerge(I) obs: 0.027 / Χ2: 1.929 / Net I/σ(I): 38.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.81-1.843.20.28621491.822193.7
1.84-1.873.30.27122421.885199.6
1.87-1.913.40.23522672.011199.5
1.91-1.953.40.17322572.289199.9
1.95-1.993.50.14622912.002199.9
1.99-2.043.60.1222342.0351100
2.04-2.093.70.10122832.124199.9
2.09-2.153.70.09122512.1311100
2.15-2.213.70.07523012.2141100
2.21-2.283.70.07122712.762199.9
2.28-2.363.70.05822512.2211100
2.36-2.463.70.05222922.3441100
2.46-2.573.70.04822962.4181100
2.57-2.73.80.04222872.221100
2.7-2.873.80.03222611.7771100
2.87-3.093.80.02622811.506199.9
3.09-3.413.70.02622961.9291100
3.41-3.93.80.0222871.4761100
3.9-4.913.80.01423030.842199.9
4.91-503.70.01222760.688197.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IGI

2igi


Resolution: 1.812→26.115 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.06
RfactorNum. reflection% reflection
Rfree0.213 2000 4.43 %
Rwork0.1933 --
obs0.1941 45179 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.38 Å2 / Biso mean: 24.9434 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: final / Resolution: 1.812→26.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 140 15 201 2964
Biso mean--72.07 32.23 -
Num. residues----325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8121-1.85740.2291340.22252886302093
1.8574-1.90760.21451420.23193092323499
1.9076-1.96380.2891430.238130543197100
1.9638-2.02710.2431420.202530813223100
2.0271-2.09950.23441440.193531263270100
2.0995-2.18360.21231440.198130893233100
2.1836-2.28290.23171430.207330823225100
2.2829-2.40320.2271430.202631023245100
2.4032-2.55360.22991450.207931183263100
2.5536-2.75060.21131430.204930873230100
2.7506-3.0270.20811440.194231193263100
3.027-3.46420.21211430.185830883231100
3.4642-4.36120.18491450.168431333278100
4.3612-26.11810.19271450.17883122326798

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