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

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Basic information

Entry
Database: PDB / ID: 6ozn
TitleCrystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 15 min soak in 10 mM Mn2+
Components
  • DNA/RNA (5'-R(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
  • Endonuclease V
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) / Endonuclease V
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_alt_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_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_alt_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

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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(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
D: DNA/RNA (5'-R(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,63725
Polymers70,6844
Non-polymers1,95321
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-97 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.402, 72.936, 155.354
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
11(chain D and (resseq 9:10 or resseq 13:23))
21(chain C and (resseq 9:10 or resseq 13:23))
12(chain A and (resseq 9:10 or resseq 12:22 or resseq...
22(chain B and (resseq 9:10 or resseq 12:22 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain D and (resseq 9:10 or resseq 13:23))D9 - 10
121(chain D and (resseq 9:10 or resseq 13:23))D13 - 23
211(chain C and (resseq 9:10 or resseq 13:23))C9 - 10
221(chain C and (resseq 9:10 or resseq 13:23))C13 - 23
112(chain A and (resseq 9:10 or resseq 12:22 or resseq...A9 - 10
122(chain A and (resseq 9:10 or resseq 12:22 or resseq...A12 - 22
132(chain A and (resseq 9:10 or resseq 12:22 or resseq...A0
142(chain A and (resseq 9:10 or resseq 12:22 or resseq...A7 - 251
152(chain A and (resseq 9:10 or resseq 12:22 or resseq...A7 - 251
162(chain A and (resseq 9:10 or resseq 12:22 or resseq...A7 - 251
172(chain A and (resseq 9:10 or resseq 12:22 or resseq...A7 - 251
182(chain A and (resseq 9:10 or resseq 12:22 or resseq...A7 - 251
192(chain A and (resseq 9:10 or resseq 12:22 or resseq...A7 - 251
212(chain B and (resseq 9:10 or resseq 12:22 or resseq...B9 - 10
222(chain B and (resseq 9:10 or resseq 12:22 or resseq...B12 - 22
232(chain B and (resseq 9:10 or resseq 12:22 or resseq...B24 - 54
242(chain B and (resseq 9:10 or resseq 12:22 or resseq...B56
252(chain B and (resseq 9:10 or resseq 12:22 or resseq...B7 - 251
262(chain B and (resseq 9:10 or resseq 12:22 or resseq...B7 - 251
272(chain B and (resseq 9:10 or resseq 12:22 or resseq...B7 - 251
282(chain B and (resseq 9:10 or resseq 12:22 or resseq...B7 - 251

NCS ensembles :
ID
1
2

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Components

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Protein / DNA/RNA hybrid , 2 types, 4 molecules ABCD

#1: Protein Endonuclease V


Mass: 28048.461 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(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')


Mass: 7293.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 206 molecules

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


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsChains C and D are partially cleaved between residues 11 and 12. Conformation A represents the ...Chains C and D are partially cleaved between residues 11 and 12. Conformation A represents the substrate state. Conformation B represents the product state.

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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: 2.83 Å3/Da / Density % sol: 56.49 %
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: Jul 11, 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: 1.9→41.92 Å / Num. obs: 63360 / % possible obs: 97.8 % / Redundancy: 1 % / Biso Wilson estimate: 29.48 Å2 / Net I/σ(I): 10.3 / Num. measured all: 63360
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 1 % / Num. unique obs: 3273 / % possible all: 79.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.503 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.28
RfactorNum. reflection% reflection
Rfree0.2214 3184 5.04 %
Rwork0.1916 --
obs0.1931 63177 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.79 Å2 / Biso mean: 52.2003 Å2 / Biso min: 19.83 Å2
Refinement stepCycle: final / Resolution: 1.9→35.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 632 103 185 4730
Biso mean--72 47.38 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074785
X-RAY DIFFRACTIONf_angle_d0.9956557
X-RAY DIFFRACTIONf_chiral_restr0.056768
X-RAY DIFFRACTIONf_plane_restr0.005726
X-RAY DIFFRACTIONf_dihedral_angle_d16.7582816
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D276X-RAY DIFFRACTION10.974TORSIONAL
12C276X-RAY DIFFRACTION10.974TORSIONAL
21A2110X-RAY DIFFRACTION10.974TORSIONAL
22B2110X-RAY DIFFRACTION10.974TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8993-1.92760.38281060.47251918202472
1.9276-1.95770.4061430.40172466260994
1.9577-1.98980.41611470.36932488263595
1.9898-2.02410.38951540.34372525267997
2.0241-2.0610.35271300.31162547267796
2.061-2.10060.28051020.28112591269396
2.1006-2.14350.31711180.25092610272898
2.1435-2.19010.22861640.22162558272298
2.1901-2.2410.27091460.22422604275098
2.241-2.2970.24791420.21362612275499
2.297-2.35910.22291280.186626772805100
2.3591-2.42850.22831410.181726572798100
2.4285-2.50690.24781330.177726542787100
2.5069-2.59650.20811390.178226492788100
2.5965-2.70040.24711690.184126462815100
2.7004-2.82320.241340.206326762810100
2.8232-2.9720.25941210.210226852806100
2.972-3.15810.23371460.19826892835100
3.1581-3.40180.23041640.182126782842100
3.4018-3.74380.18571350.163926992834100
3.7438-4.28470.15641480.14427352883100
4.2847-5.39530.17821300.135327572887100
5.3953-35.50910.16611440.17672872301699
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)
16.60544.06-3.6674.9448-2.61023.1506-0.1852-0.0672-0.2939-0.1007-0.0069-0.37640.2351-0.02550.22020.41340.03030.0020.1888-0.07220.159136.19191.692644.2305
26.3593-1.78340.5214.27710.53944.8116-0.28550.99110.7014-0.94830.0554-0.3078-0.4849-0.13690.19530.5704-0.0104-0.0430.36550.03730.251522.28069.62934.8104
32.47180.0447-0.82021.6329-0.03651.3118-0.03820.03640.257-0.14540.0641-0.0087-0.1814-0.1133-0.03320.45760.0155-0.01170.25130.00280.211827.48256.720141.743
41.8497-0.53970.54852.6757-0.00572.7470.00070.1991-0.0563-0.54010.00590.00760.3053-0.09930.01410.58-0.05850.01130.23690.00840.20227.476-7.569433.4743
55.2787-2.7612-2.73094.11025.46447.7509-0.4171-0.66870.39890.23150.04070.9179-0.1753-0.46280.21640.72320.1673-0.09010.5536-0.08310.6078-8.890913.1502-4.3938
62.7716-0.12380.13441.8666-0.042.9773-0.1157-0.22740.25820.44240.03520.0161-0.32540.05770.03370.64410.0054-0.06670.28320.00550.22558.97775.0137-6.7564
74.1141-0.08960.0674.2398-1.19545.0220.0159-0.5562-0.50160.89990.13840.36740.5942-0.4106-0.13740.8092-0.0770.04490.36250.05320.32392.821-10.76081.2877
83.52220.3110.75742.62134.61938.5753-0.177-0.20920.3070.92550.1831-0.4361-0.42310.7413-0.10780.9636-0.0411-0.20950.4496-0.01110.317518.62467.41665.0371
92.23451.13344.08492.7491.03847.1141-0.58730.16090.2808-0.55130.20450.372-0.8635-0.17420.34760.66180.0784-0.05650.3823-0.00250.283419.19340.576419.8877
103.2723-2.45174.05083.0545-1.65827.2958-0.0888-0.01640.1726-0.13420.0056-0.0419-0.7621-0.13050.04280.7856-0.0493-0.02420.43850.01930.320414.40560.734815.7316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 46 )A7 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 71 )A47 - 71
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 154 )A72 - 154
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 251 )A155 - 251
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 27 )B7 - 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 9 through 23 )C9 - 23
10X-RAY DIFFRACTION10chain 'D' and (resid 9 through 23 )D9 - 23

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