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

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Basic information

Entry
Database: PDB / ID: 6ozl
TitleCrystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 2 min soak in 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 / Nucleic acid hydrolysis / RNA recognition / metal ion dependent catalysis / DNA damage / adenosine deamination
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 / L(+)-TARTARIC ACID / 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: 2.1 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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)71,56114
Polymers70,6844
Non-polymers87710
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-82 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.621, 72.519, 155.764
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 A and (resseq 8:10 or resseq 13:14 or resseq...
21(chain B and (resseq 8:10 or resseq 13:14 or resseq...
12(chain D and resseq 9:23)
22chain C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGPROPRO(chain A and (resseq 8:10 or resseq 13:14 or resseq...AA8 - 108 - 10
121THRTHRLEULEU(chain A and (resseq 8:10 or resseq 13:14 or resseq...AA13 - 1413 - 14
131TRPTRPALAALA(chain A and (resseq 8:10 or resseq 13:14 or resseq...AA17 - 2217 - 22
141LEULEUVALVAL(chain A and (resseq 8:10 or resseq 13:14 or resseq...AA24 - 5324 - 53
151SERSERSERSER(chain A and (resseq 8:10 or resseq 13:14 or resseq...AA5454
161GLUGLULEULEU(chain A and (resseq 8:10 or resseq 13:14 or resseq...AA7 - 2517 - 251
171GLUGLULEULEU(chain A and (resseq 8:10 or resseq 13:14 or resseq...AA7 - 2517 - 251
181GLUGLULEULEU(chain A and (resseq 8:10 or resseq 13:14 or resseq...AA7 - 2517 - 251
211ARGARGPROPRO(chain B and (resseq 8:10 or resseq 13:14 or resseq...BB8 - 108 - 10
221THRTHRLEULEU(chain B and (resseq 8:10 or resseq 13:14 or resseq...BB13 - 1413 - 14
231TRPTRPALAALA(chain B and (resseq 8:10 or resseq 13:14 or resseq...BB17 - 2217 - 22
241LEULEUVALVAL(chain B and (resseq 8:10 or resseq 13:14 or resseq...BB24 - 5324 - 53
251SERSERSERSER(chain B and (resseq 8:10 or resseq 13:14 or resseq...BB5454
261ARGARGLEULEU(chain B and (resseq 8:10 or resseq 13:14 or resseq...BB8 - 2518 - 251
271ARGARGLEULEU(chain B and (resseq 8:10 or resseq 13:14 or resseq...BB8 - 2518 - 251
281ARGARGLEULEU(chain B and (resseq 8:10 or resseq 13:14 or resseq...BB8 - 2518 - 251
112CCUU(chain D and resseq 9:23)DD9 - 239 - 23
212CCUUchain CCC9 - 239 - 23

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 , 6 types, 164 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.25 Å3/Da / Density % sol: 62.12 %
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 6, 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: 2.1→42.43 Å / Num. obs: 47563 / % possible obs: 95.8 % / Redundancy: 1 % / Biso Wilson estimate: 35.97 Å2 / Net I/σ(I): 8.9 / Num. measured all: 47563
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 1 % / Num. unique obs: 2928 / % possible all: 72.8

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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: 2.1→35.824 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 25.16
RfactorNum. reflection% reflection
Rfree0.2169 2365 4.99 %
Rwork0.1759 --
obs0.1779 47439 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 173.69 Å2 / Biso mean: 53.5328 Å2 / Biso min: 22.44 Å2
Refinement stepCycle: final / Resolution: 2.1→35.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 650 47 154 4634
Biso mean--72.86 49.52 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084677
X-RAY DIFFRACTIONf_angle_d0.9646478
X-RAY DIFFRACTIONf_chiral_restr0.054767
X-RAY DIFFRACTIONf_plane_restr0.006721
X-RAY DIFFRACTIONf_dihedral_angle_d13.9172764
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1896X-RAY DIFFRACTION5.565TORSIONAL
12B1896X-RAY DIFFRACTION5.565TORSIONAL
21D324X-RAY DIFFRACTION5.565TORSIONAL
22C324X-RAY DIFFRACTION5.565TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0983-2.14120.3701980.31421930202871
2.1412-2.18770.33661040.27672222232681
2.1877-2.23860.3091170.26412402251987
2.2386-2.29460.26061260.24272543266993
2.2946-2.35660.28571420.2232656279897
2.3566-2.42590.26491320.213427402872100
2.4259-2.50420.28571460.202827282874100
2.5042-2.59370.24081530.203927342887100
2.5937-2.69750.24861820.204526962878100
2.6975-2.82020.27361570.207327412898100
2.8202-2.96890.32031410.208527652906100
2.9689-3.15480.241410.201127722913100
3.1548-3.39820.24091250.179727852910100
3.3982-3.73980.18831610.15827802941100
3.7398-4.28020.16711510.139428022953100
4.2802-5.38970.14761340.127528562990100
5.3897-35.82890.19711550.15742922307798
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)
18.16116.2411-4.9346.8365-5.19385.8565-0.1951-0.4438-0.5604-0.1591-0.3914-0.56630.23690.39710.57150.37030.07840.03450.2053-0.07540.246836.95321.080944.9198
24.16530.1213-1.28242.3447-0.64142.5868-0.07290.20340.3683-0.20660.07990.059-0.2171-0.2348-0.03390.43830.0217-0.03730.3003-0.01110.251627.29016.97640.3244
32.7598-0.3210.49373.46820.12024.08090.02730.2604-0.0901-0.6928-0.05340.07370.4531-0.07830.02510.5565-0.00920.02340.25450.01970.233728.1784-8.066333.4087
46.2205-4.0589-3.23534.34124.41486.83390.09170.4039-0.0363-0.226-0.52050.77690.0277-0.63590.65220.3265-0.085-0.0220.28170.02540.5392-0.14912.7605-11.1349
57.0838-1.4567-2.35396.94242.01438.06660.0113-0.72820.56020.68290.02950.1243-0.3550.251-0.12840.2895-0.0349-0.07660.3215-0.0460.267513.54239.65320.5468
66.3006-0.3269-2.31855.77733.29815.09940.0952-0.1230.73690.43390.1265-0.2728-0.14120.2793-0.19860.36240.0338-0.0920.30810.11020.169912.53867.9874-2.3627
74.8312-0.6519-4.70833.43350.64924.6110.4619-0.75861.57470.04820.23280.2921-1.01680.5118-0.72120.3767-0.0018-0.08040.4758-0.03570.4829.730613.07-7.7051
83.28640.057-4.80424.8670.10187.6823-0.02440.10450.17680.18070.01130.3983-0.0114-0.1722-0.0090.32220.0102-0.04940.2666-0.00860.26655.33362.9342-8.8088
95.96380.4298-0.32215.8019-1.19196.93760.1793-0.7375-0.68831.19960.11030.91550.8454-0.6093-0.31680.8683-0.1180.18770.48380.06920.5650.0686-12.24364.6348
103.56021.43831.89335.11070.83023.77850.0634-0.0664-0.0680.6728-0.0289-0.26290.27020.4253-0.0580.3870.0281-0.01050.30490.02330.201313.5129-1.3872-0.7635
110.65460.10332.28483.817-0.02336.4596-0.43610.19720.3416-0.49250.09210.5654-0.4892-0.21920.29360.45970.0759-0.03090.3648-0.03410.35919.67750.192419.4047
121.5595-1.46193.61144.2266-1.14358.3798-0.3726-0.29750.16050.33450.0855-0.0524-0.792-0.27050.20920.5366-0.07040.02450.39180.00630.311413.71180.538715.4854
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 154 )A47 - 154
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 251 )A155 - 251
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 46 )B8 - 46
5X-RAY DIFFRACTION5chain 'B' and (resid 47 through 71 )B47 - 71
6X-RAY DIFFRACTION6chain 'B' and (resid 72 through 95 )B72 - 95
7X-RAY DIFFRACTION7chain 'B' and (resid 96 through 114 )B96 - 114
8X-RAY DIFFRACTION8chain 'B' and (resid 115 through 154 )B115 - 154
9X-RAY DIFFRACTION9chain 'B' and (resid 155 through 206 )B155 - 206
10X-RAY DIFFRACTION10chain 'B' and (resid 207 through 251 )B207 - 251
11X-RAY DIFFRACTION11chain 'C' and (resid 9 through 23 )C9 - 23
12X-RAY DIFFRACTION12chain 'D' and (resid 8 through 23 )D8 - 23

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