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- PDB-6j7z: Human mitochondrial Oligoribonuclease in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 6j7z
TitleHuman mitochondrial Oligoribonuclease in complex with RNA
Components
  • Oligoribonuclease, mitochondrial
  • RNA (5'-R(P*UP*U)-3')
KeywordsHYDROLASE / Exoribonuclease / Mitochonrial Oligoribonuclease
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-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / RNA / Oligoribonuclease, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 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: 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

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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: RNA (5'-R(P*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8646
Polymers43,6233
Non-polymers2413
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-38 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.192, 125.892, 86.008
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-454-

HOH

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Components

#1: Protein Oligoribonuclease, mitochondrial / RNA exonuclease 2 homolog / Small fragment nuclease


Mass: 21527.777 Da / Num. of mol.: 2 / Mutation: D199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REXO2, SFN, SMFN, CGI-114 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y3B8, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*UP*U)-3')


Mass: 567.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CIT / 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


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
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: Sep 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 31548 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.37 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.033 / Rrim(I) all: 0.083 / Χ2: 2.932 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.036.90.50815400.9260.2080.5491.519100
2.03-2.076.90.41515460.9410.170.4491.635100
2.07-2.116.90.36915900.960.1510.3991.622100
2.11-2.156.90.33215540.9620.1350.3591.769100
2.15-2.26.90.27515820.9690.1130.2981.92199.9
2.2-2.256.90.23715500.980.0970.2562.113100
2.25-2.316.90.21215600.9810.0870.2292.354100
2.31-2.376.80.18615720.9840.0770.2012.47499.9
2.37-2.446.80.16815690.9870.070.1822.586100
2.44-2.526.80.14515670.990.060.1572.736100
2.52-2.616.80.1315900.9910.0540.1412.982100
2.61-2.716.70.11215620.9920.0470.1223.20799.9
2.71-2.846.60.09815650.9930.0410.1063.45499.9
2.84-2.996.50.08715810.9950.0370.0953.823100
2.99-3.176.10.07916090.9960.0350.0874.243100
3.17-3.425.90.06815730.9960.030.0754.447100
3.42-3.7660.06115940.9950.0270.0674.56199.9
3.76-4.3160.05516020.9970.0240.064.39499.7
4.31-5.4360.05216380.9970.0230.0574.29999.8
5.43-505.60.04616040.9970.020.053.66394.2

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Processing

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

2igi


Resolution: 2.005→27.405 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.33
RfactorNum. reflection% reflection
Rfree0.2277 2000 6.34 %
Rwork0.2058 --
obs0.2072 31521 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.31 Å2 / Biso mean: 45.4916 Å2 / Biso min: 19.3 Å2
Refinement stepCycle: final / Resolution: 2.005→27.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 40 15 124 2808
Biso mean--75.28 50.11 -
Num. residues----323
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 (%)
2.0052-2.05540.25541380.23672032217097
2.0554-2.11090.24361410.234920852226100
2.1109-2.1730.26881420.233120922234100
2.173-2.24310.25091420.225621022244100
2.2431-2.32330.27321410.228720872228100
2.3233-2.41620.27751410.230620752216100
2.4162-2.52610.27481440.228321242268100
2.5261-2.65920.22861430.228621062249100
2.6592-2.82560.24671430.232821232266100
2.8256-3.04360.27921430.22521182261100
3.0436-3.34940.22511440.218621182262100
3.3494-3.83290.19061460.18721432289100
3.8329-4.82470.17411460.16721562302100
4.8247-27.40710.23771460.19872160230696
Refinement TLS params.Method: refined / Origin x: 30.1829 Å / Origin y: 150.6185 Å / Origin z: -0.0866 Å
111213212223313233
T0.2505 Å2-0.036 Å20.0058 Å2-0.2225 Å20.0277 Å2--0.2004 Å2
L2.3456 °2-0.3306 °2-0.504 °2-0.5207 °20.1412 °2--1.2479 °2
S0.0586 Å °-0.1442 Å °0.2032 Å °0.096 Å °0.0184 Å °-0.1085 Å °-0.2208 Å °0.0775 Å °-0.053 Å °
Refinement TLS groupSelection details: all

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