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

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Basic information

Entry
Database: PDB / ID: 6ozj
TitleCrystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine in the absence of divalent cation
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 / Nucleic acid hydrolysis / RNA recognition / metal ion dependent catalysis / DNA damage / adenosine deamination
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) / Endonuclease V
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.247 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.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(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)71,52915
Polymers70,6844
Non-polymers84511
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-48 kcal/mol
Surface area24760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.341, 73.582, 154.187
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 8:22 or resseq 24:37 or resseq...
22(chain B and (resseq 8:22 or resseq 24:37 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain DD9 - 23
211chain CC9 - 23
112(chain A and (resseq 8:22 or resseq 24:37 or resseq...A8 - 22
122(chain A and (resseq 8:22 or resseq 24:37 or resseq...A24 - 37
132(chain A and (resseq 8:22 or resseq 24:37 or resseq...A0
142(chain A and (resseq 8:22 or resseq 24:37 or resseq...A55
152(chain A and (resseq 8:22 or resseq 24:37 or resseq...A7 - 250
162(chain A and (resseq 8:22 or resseq 24:37 or resseq...A7 - 250
172(chain A and (resseq 8:22 or resseq 24:37 or resseq...A7 - 250
182(chain A and (resseq 8:22 or resseq 24:37 or resseq...A7 - 250
192(chain A and (resseq 8:22 or resseq 24:37 or resseq...A7 - 250
212(chain B and (resseq 8:22 or resseq 24:37 or resseq...B8 - 22
222(chain B and (resseq 8:22 or resseq 24:37 or resseq...B24 - 37
232(chain B and (resseq 8:22 or resseq 24:37 or resseq...B39 - 40
242(chain B and (resseq 8:22 or resseq 24:37 or resseq...B0
252(chain B and (resseq 8:22 or resseq 24:37 or resseq...B4 - 253
262(chain B and (resseq 8:22 or resseq 24:37 or resseq...B4 - 253
272(chain B and (resseq 8:22 or resseq 24:37 or resseq...B4 - 253
282(chain B and (resseq 8:22 or resseq 24:37 or resseq...B4 - 253
292(chain B and (resseq 8:22 or resseq 24:37 or resseq...B4 - 253
2102(chain B and (resseq 8:22 or resseq 24:37 or resseq...B4 - 253

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 , 5 types, 379 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 61.28 %
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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2015
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: 2.25→48.92 Å / Num. obs: 40002 / % possible obs: 99.8 % / Redundancy: 1 % / Biso Wilson estimate: 30.52 Å2 / Net I/σ(I): 15 / Num. measured all: 40002
Reflection shell
Resolution (Å)Redundancy (%)Num. measured allNum. unique obsDiffraction-IDNet I/σ(I) obs% possible all
2.25-2.3213554355414.198.3
8.99-48.921715715135.999.3

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.247→42.873 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.82
RfactorNum. reflection% reflection
Rfree0.1938 3820 5.05 %
Rwork0.1564 --
obs0.1583 39920 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.33 Å2 / Biso mean: 34.8762 Å2 / Biso min: 11.55 Å2
Refinement stepCycle: final / Resolution: 2.247→42.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 630 52 368 4884
Biso mean--65.43 41.92 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074727
X-RAY DIFFRACTIONf_angle_d0.9516527
X-RAY DIFFRACTIONf_chiral_restr0.055762
X-RAY DIFFRACTIONf_plane_restr0.005732
X-RAY DIFFRACTIONf_dihedral_angle_d18.0972805
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D324X-RAY DIFFRACTION6.664TORSIONAL
12C324X-RAY DIFFRACTION6.664TORSIONAL
21A1964X-RAY DIFFRACTION6.664TORSIONAL
22B1964X-RAY DIFFRACTION6.664TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2466-2.2750.21391180.19582518263696
2.275-2.30490.22651020.191727192821100
2.3049-2.33650.24011320.189426752807100
2.3365-2.36990.20721300.188426722802100
2.3699-2.40520.20361450.181226922837100
2.4052-2.44280.21711290.179926642793100
2.4428-2.48290.25251460.17926372783100
2.4829-2.52570.22951230.187526762799100
2.5257-2.57160.23511350.168226822817100
2.5716-2.62110.21861250.177426852810100
2.6211-2.67450.21380.166726452783100
2.6745-2.73270.24311580.179326722830100
2.7327-2.79630.21941620.18826492811100
2.7963-2.86620.25051500.191826502800100
2.8662-2.94360.22121590.185626582817100
2.9436-3.03020.23441320.17426612793100
3.0302-3.1280.21231390.175326582797100
3.128-3.23980.17251780.16626352813100
3.2398-3.36940.19471440.154926572801100
3.3694-3.52270.2061560.150226642820100
3.5227-3.70840.17651550.153426432798100
3.7084-3.94050.17721220.135726792801100
3.9405-4.24460.15841160.128126972813100
4.2446-4.67120.15081820.114926302812100
4.6712-5.34610.17941050.120726962801100
5.3461-6.73130.17061890.1526182807100
6.7313-42.8810.17991500.152826532803100
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)
16.41152.5345-3.04548.4556-5.74544.55190.01010.00010.2277-0.3963-0.0241-0.5196-0.0340.5318-0.02190.2253-0.03580.04620.1709-0.08420.31846.18369.282237.7413
23.12290.2771-0.0493.9698-1.52614.007-0.15730.1360.0324-0.31920.11550.01360.1037-0.13310.06430.1884-0.02080.01630.1522-0.06970.150724.7457-0.421142.7509
33.1046-0.1615-1.72542.00210.26061.93970.09970.20430.344-0.17490.06610.0756-0.3409-0.1943-0.2520.24080.0097-0.03630.17760.02450.1925.82149.204239.0228
42.4246-1.325-1.03993.80591.16992.4877-0.03760.08010.071-0.26960.1097-0.13730.05970.0299-0.08490.1795-0.0274-0.00230.10310.02550.141333.2613-1.171839.1773
59.0148-1.15161.41553.26380.27013.46440.07250.2257-0.3404-0.4864-0.040.08450.418-0.206-0.05650.3894-0.04780.00620.13650.02780.176231.7774-16.656330.7154
63.85011.05122.40443.86570.20935.02130.0414-0.0318-0.1027-0.01890.02450.13770.4456-0.3338-0.05410.2026-0.02060.0340.12660.00720.146926.2535-9.456639.8757
78.63823.084-3.16623.0585-4.45187.9838-0.21430.59610.8945-0.56260.39510.7555-1.0854-0.5771-0.1750.50280.0387-0.14940.35590.01640.365916.92386.814730.033
84.6417-2.6507-0.69853.17631.14062.1014-0.0846-0.09590.035-0.1680.04190.5254-0.0013-0.32330.10480.1289-0.0104-0.05450.22280.07390.3719-0.24144.3299-9.2384
94.0676-1.0186-0.75223.20540.95733.4542-0.1385-0.39860.37640.2360.2377-0.1021-0.18290.2543-0.13730.14380.0181-0.05980.21830.02940.2113.28648.5504-0.5418
108.5764-1.6878-6.52282.2151.25184.970.1624-0.41740.7482-0.05110.15640.0505-0.39470.2924-0.36930.14840.0097-0.04650.240.00760.244410.033613.1542-7.378
111.8882-0.20190.32442.6559-0.39672.07650.0023-0.2584-0.30750.23480.1420.39340.34-0.3707-0.11410.1953-0.0413-0.01320.25390.05410.29072.7395-5.8337-1.004
124.0074-0.81371.6564.0991-0.80475.90720.1258-0.155-0.4081-0.04870.1090.14990.7240.0707-0.23760.21360.0045-0.02230.16020.030.23019.2441-8.1179-5.1532
135.4188-1.6556-3.33746.49380.47032.12970.051-0.32180.43010.8930.1536-0.5834-0.10630.5937-0.27480.22370.0134-0.12490.3705-0.01650.301520.34627.78725.3221
142.74261.13373.41531.54290.44974.5829-0.14550.17930.00480.05640.16910.1389-0.2979-0.0766-0.04260.2570.02260.01180.25130.03140.219220.1201-0.605418.9685
150.24810.18630.99782.2848-0.25194.03-0.3808-0.1578-0.1280.25150.2896-0.0488-0.1842-0.05580.07040.21720.01770.01920.33920.03170.281915.9231-0.399515.4849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 27 )A7 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 71 )A28 - 71
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 114 )A72 - 114
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 166 )A115 - 166
5X-RAY DIFFRACTION5chain 'A' and (resid 167 through 206 )A167 - 206
6X-RAY DIFFRACTION6chain 'A' and (resid 207 through 233 )A207 - 233
7X-RAY DIFFRACTION7chain 'A' and (resid 234 through 250 )A234 - 250
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 46 )B4 - 46
9X-RAY DIFFRACTION9chain 'B' and (resid 47 through 95 )B47 - 95
10X-RAY DIFFRACTION10chain 'B' and (resid 96 through 114 )B96 - 114
11X-RAY DIFFRACTION11chain 'B' and (resid 115 through 206 )B115 - 206
12X-RAY DIFFRACTION12chain 'B' and (resid 207 through 233 )B207 - 233
13X-RAY DIFFRACTION13chain 'B' and (resid 234 through 253 )B234 - 253
14X-RAY DIFFRACTION14chain 'C' and (resid 9 through 23 )C9 - 23
15X-RAY DIFFRACTION15chain 'D' and (resid 9 through 23 )D9 - 23

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