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- PDB-6ozp: Crystal structure of Mus musculus (Mm) Endonuclease V in complex ... -

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Basic information

Entry
Database: PDB / ID: 6ozp
TitleCrystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 180 min soak in 10 mM Mn2+
Components
  • DNA/RNA (5'-R(*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*A)-3')
  • Endonuclease V
  • RNA (5'-R(P*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
KeywordsHYDROLASE/RNA / Nucleic acid hydrolysis / RNA recognition / metal ion dependent catalysis / DNA damage / adenosine deamination / HYDROLASE-RNA complex
Function / homology
Function and homology information


DNA endonuclease activity, producing 5'-phosphomonoesters / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / cytoplasmic stress granule / single-stranded RNA binding / DNA repair / nucleolus / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function
Endonuclease V / Endonuclease V / archaeoglobus fulgidus dsm 4304 fold / archaeoglobus fulgidus dsm 4304 superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10) / Endonuclease V
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSamara, N.L. / Yang, W.
CitationJournal: Mol.Cell / Year: 2019
Title: Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Authors: Wu, J. / Samara, N.L. / Kuraoka, I. / Yang, W.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease V
B: Endonuclease V
c: DNA/RNA (5'-R(*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*A)-3')
C: RNA (5'-R(P*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
d: DNA/RNA (5'-R(*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*A)-3')
D: RNA (5'-R(P*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,91230
Polymers68,9126
Non-polymers2,00024
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-84 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.031, 73.006, 155.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA/RNA hybrid / RNA chain , 3 types, 6 molecules ABcdCD

#1: Protein Endonuclease V


Mass: 27207.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Endov / Production host: Escherichia coli (E. coli)
References: UniProt: Q8C9A2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: DNA/RNA hybrid DNA/RNA (5'-R(*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*A)-3')


Mass: 3474.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')


Mass: 3774.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 344 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 3.18 Å3/Da / Density % sol: 61.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium sodium tartrate, 20-25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 17, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→38.94 Å / Num. obs: 56317 / % possible obs: 94.2 % / Redundancy: 1 % / Biso Wilson estimate: 26.67 Å2 / Net I/σ(I): 10.1 / Num. measured all: 56317
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 1 % / Num. unique obs: 2410 / % possible all: 58

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→36.483 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2013 2848 5.07 %
Rwork0.1749 --
obs0.1763 56185 94.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→36.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 672 103 320 4871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074768
X-RAY DIFFRACTIONf_angle_d0.936570
X-RAY DIFFRACTIONf_dihedral_angle_d15.872815
X-RAY DIFFRACTIONf_chiral_restr0.057772
X-RAY DIFFRACTIONf_plane_restr0.006726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9604-1.99420.2949600.28061394X-RAY DIFFRACTION49
1.9942-2.03050.41831040.31442302X-RAY DIFFRACTION82
2.0305-2.06950.32831300.29652384X-RAY DIFFRACTION86
2.0695-2.11180.30381430.28072499X-RAY DIFFRACTION90
2.1118-2.15770.26361400.2412542X-RAY DIFFRACTION91
2.1577-2.20790.24911430.21872630X-RAY DIFFRACTION94
2.2079-2.26310.2451480.21412650X-RAY DIFFRACTION95
2.2631-2.32430.23661310.20352742X-RAY DIFFRACTION97
2.3243-2.39270.24631630.19052741X-RAY DIFFRACTION98
2.3927-2.46990.23281590.18852779X-RAY DIFFRACTION100
2.4699-2.55810.20951350.17882844X-RAY DIFFRACTION100
2.5581-2.66050.23491850.16922770X-RAY DIFFRACTION100
2.6605-2.78160.20811550.16652852X-RAY DIFFRACTION100
2.7816-2.92810.19531380.18092844X-RAY DIFFRACTION100
2.9281-3.11150.18931230.17542856X-RAY DIFFRACTION100
3.1115-3.35160.18921440.1682836X-RAY DIFFRACTION100
3.3516-3.68860.15371430.14992875X-RAY DIFFRACTION100
3.6886-4.22170.15781730.1362860X-RAY DIFFRACTION100
4.2217-5.31620.15611440.12842925X-RAY DIFFRACTION100
5.3162-36.4890.19871870.17643012X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.93474.093-3.15275.3245-2.99963.3871-0.1108-0.211-0.39530.0017-0.1542-0.49190.08170.11970.28120.15470.0352-0.00330.1312-0.06790.147836.31911.19445.3732
22.62970.016-0.88632.179-0.04882.0904-0.05820.0980.2365-0.11290.05680.0568-0.2286-0.212-0.01370.20510.0195-0.02320.19670.00510.195126.75367.187640.3091
31.9238-0.60530.62823.3957-0.32553.79430.03140.1972-0.13-0.50090.01160.00280.4365-0.0098-0.03870.3089-0.02330.01450.14080.00450.195430.222-11.485334.2019
47.35130.0624-0.60767.6497-3.23297.6058-0.11290.31590.6887-0.87860.37140.2786-0.1663-0.3353-0.2830.31780.0043-0.07950.28490.02340.288216.6188.152731.1517
56.8614-4.6527-2.63626.63283.50074.6303-0.0750.1971-0.15460.1281-0.24320.5525-0.0516-0.45610.32370.2597-0.0219-0.04250.1980.06310.2105-0.28062.6145-10.9745
63.2921-0.5322-0.25291.99240.14893.2387-0.0954-0.14710.31050.24530.0479-0.0092-0.3460.08390.0060.29410.0059-0.05430.175-0.00260.20739.32767.5393-4.8362
73.6491-0.2143-0.41854.0519-0.62784.6134-0.0181-0.4656-0.53230.73630.11110.36530.7173-0.3566-0.0470.4616-0.06960.04560.26660.0480.30193.1798-10.87831.1238
85.08440.56550.85916.38121.36995.2156-0.0050.11440.34190.7387-0.03820.0031-0.27660.3485-0.06210.382-0.0124-0.11290.2760.02040.210219.2367.42064.9314
94.81641.11662.47845.0852-2.4623.2862-0.28491.1868-0.3346-1.55310.4474-1.88640.52381.78550.03140.368-0.0440.21860.6513-0.11080.567338.95480.880227.4814
100.7490.40680.23873.21330.11554.767-0.13380.03110.1312-0.11340.00910.5215-0.3096-0.33650.11180.30350.031-0.07460.34340.02130.312515.06810.043517.4544
111.3756-2.67591.30095.222-2.51571.2298-0.3945-1.27070.14381.720.09172.26070.356-2.2619-0.03690.56240.02360.22881.0507-0.10260.749-4.51662.56467.1837
121.4656-0.9826-0.39243.83490.32314.68290.1976-0.11890.058-0.2633-0.1076-0.1415-0.32050.245-0.06890.2886-0.0389-0.03970.3150.00450.23119.112-0.08818.3793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 154 )
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 233 )
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 252 )
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 46 )
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 154 )
7X-RAY DIFFRACTION7chain 'B' and (resid 155 through 233 )
8X-RAY DIFFRACTION8chain 'B' and (resid 234 through 251 )
9X-RAY DIFFRACTION9chain 'C' and (resid 8 through 11 )
10X-RAY DIFFRACTION10chain 'C' and (resid 12 through 23 )
11X-RAY DIFFRACTION11chain 'D' and (resid 8 through 11 )
12X-RAY DIFFRACTION12chain 'D' and (resid 12 through 23 )

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