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

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Basic information

Entry
Database: PDB / ID: 6ozs
TitleCrystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 90 min soak in 10 mM Mg2+
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


RNA endonuclease activity, producing 5'-phosphomonoesters / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / 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: 2.41 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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: 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)70,87223
Polymers69,3126
Non-polymers1,55917
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-115 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.086, 73.257, 155.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain D
21chain C
12(chain A and (resseq 9:11 or resseq 13:15 or resseq...
22(chain B and (resseq 9:11 or resseq 13:15 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain DD8 - 11
211chain CC8 - 11
112(chain A and (resseq 9:11 or resseq 13:15 or resseq...A9 - 11
122(chain A and (resseq 9:11 or resseq 13:15 or resseq...A13 - 15
132(chain A and (resseq 9:11 or resseq 13:15 or resseq...A0
142(chain A and (resseq 9:11 or resseq 13:15 or resseq...A54
152(chain A and (resseq 9:11 or resseq 13:15 or resseq...A6 - 252
162(chain A and (resseq 9:11 or resseq 13:15 or resseq...A6 - 252
172(chain A and (resseq 9:11 or resseq 13:15 or resseq...A6 - 252
182(chain A and (resseq 9:11 or resseq 13:15 or resseq...A6 - 252
212(chain B and (resseq 9:11 or resseq 13:15 or resseq...B9 - 11
222(chain B and (resseq 9:11 or resseq 13:15 or resseq...B13 - 15
232(chain B and (resseq 9:11 or resseq 13:15 or resseq...B0
242(chain B and (resseq 9:11 or resseq 13:15 or resseq...B54
252(chain B and (resseq 9:11 or resseq 13:15 or resseq...B8 - 251
262(chain B and (resseq 9:11 or resseq 13:15 or resseq...B8 - 251
272(chain B and (resseq 9:11 or resseq 13:15 or resseq...B8 - 251
282(chain B and (resseq 9:11 or resseq 13:15 or resseq...B8 - 251

NCS ensembles :
ID
1
2

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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: 27407.730 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 , 8 types, 53 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.88 Å3/Da / Density % sol: 61.62 %
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: Jun 13, 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: 2.41→41.71 Å / Num. obs: 30469 / % possible obs: 95.6 % / Redundancy: 1 % / Biso Wilson estimate: 48.74 Å2 / Net I/σ(I): 11 / Num. measured all: 30469
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 1 % / Num. unique obs: 2341 / % possible all: 71.4

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→36.246 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 29.73
RfactorNum. reflection% reflection
Rfree0.236 1530 5.05 %
Rwork0.1909 --
obs0.1932 30306 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 199.49 Å2 / Biso mean: 39 Å2 / Biso min: 31.01 Å2
Refinement stepCycle: final / Resolution: 2.41→36.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3785 506 265 36 4592
Biso mean--97.79 59.27 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074729
X-RAY DIFFRACTIONf_angle_d1.0126508
X-RAY DIFFRACTIONf_chiral_restr0.053763
X-RAY DIFFRACTIONf_plane_restr0.006716
X-RAY DIFFRACTIONf_dihedral_angle_d16.432774
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D342X-RAY DIFFRACTION7.501TORSIONAL
12C342X-RAY DIFFRACTION7.501TORSIONAL
21A1975X-RAY DIFFRACTION7.501TORSIONAL
22B1975X-RAY DIFFRACTION7.501TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4067-2.48440.343920.28751871196369
2.4844-2.57320.32711160.27612309242585
2.5732-2.67610.30331370.26052609274696
2.6761-2.79790.24331490.25542686283599
2.7979-2.94530.3151400.235827112851100
2.9453-3.12980.30721510.219527072858100
3.1298-3.37130.27281310.200327502881100
3.3713-3.71020.22331480.182927362884100
3.7102-4.24640.22751480.166327422890100
4.2464-5.34730.21061460.15022783292999
5.3473-36.25050.19591720.18272872304499
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)
19.63136.5301-4.99457.982-4.56786.543-0.2735-0.6061-0.5127-0.1273-0.3491-0.69920.55730.34460.62810.30740.1116-0.00120.2865-0.13560.319935.47641.700144.7803
24.80470.0758-1.8573.2249-0.094.5675-0.05590.21520.3889-0.25090.07150.2733-0.2226-0.3467-0.0210.31960.0002-0.0340.371-0.01490.364225.69886.9740.9176
32.1978-0.737-0.29484.50020.70655.41840.0280.2367-0.1671-0.35630.06920.07930.2612-0.1649-0.11140.4274-0.0425-0.01140.31390.00350.379329.9316-11.381834.0808
43.103-0.47180.35674.9079-4.94454.9188-0.32330.01070.5558-1.05380.39770.72790.0165-0.9324-0.14330.6047-0.0461-0.11250.61520.00680.627915.42188.185131.389
57.80211.85631.23226.30371.69298.7392-0.1442-0.48231.308-0.0586-0.26990.7612-2.2294-1.34770.43191.15660.41-0.16480.9478-0.08480.9264-8.974612.9421-4.9748
63.9751-0.54410.39663.29190.2957.464-0.2929-0.24270.44020.83990.15110.073-1.0203-0.19290.09440.77960.061-0.05880.42620.04630.38688.79084.8077-6.9257
73.57010.2637-0.54816.9754-2.44555.05760.1402-0.7405-0.32260.91430.23290.55180.8096-0.4907-0.36010.7869-0.04630.03480.63560.02190.49332.8922-10.72421.1478
85.88571.40570.61963.44395.22998.372-0.448-0.22490.95611.34510.02-0.3662-1.11430.77030.41621.5026-0.082-0.26740.79180.03420.580318.50447.28654.744
98.80094.0016-2.88482.047-2.06273.6114-1.11140.836-0.0988-2.47611.2635-3.06521.25131.73550.13590.847-0.13110.41520.9305-0.15961.215738.0520.996727.5931
100.30250.51680.24224.4551-0.45476.5162-0.868-0.15710.8844-0.48280.06720.92-1.271-0.64440.67680.72310.1089-0.20490.8865-0.03290.700114.46670.064717.4443
112.892-2.15341.85163.02150.9314.9932-0.2991-0.70510.10752.8106-0.24032.56462.4454-1.16620.79751.77430.40040.63811.4137-0.04841.2926-4.65072.31847.3301
123.1403-0.6419-3.09876.38791.63478.92340.23290.14910.2894-0.6254-0.2253-0.0993-1.58480.2986-0.0220.707-0.0513-0.15140.6521-0.01640.455818.7179-0.118.4295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 46 )A6 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 154 )A47 - 154
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 233 )A155 - 233
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 251 )A234 - 251
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 27 )B8 - 27
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 154 )B28 - 154
7X-RAY DIFFRACTION7chain 'B' and (resid 155 through 233 )B155 - 233
8X-RAY DIFFRACTION8chain 'B' and (resid 234 through 251 )B234 - 251
9X-RAY DIFFRACTION9chain 'C' and (resid 12 through 23 )C12 - 23
10X-RAY DIFFRACTION10chain 'D' and (resid 12 through 23 )D12 - 23

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