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- PDB-6ozq: Crystal structure of Mus musculus (Mm) Endonuclease V (K155M) in ... -

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Basic information

Entry
Database: PDB / ID: 6ozq
TitleCrystal structure of Mus musculus (Mm) Endonuclease V (K155M) in complex with a 23mer RNA oligo containing an inosine after a 100 min soak in 10 mM Mn2+ and K+
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: 2.153 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_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_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_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_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)71,56816
Polymers70,6884
Non-polymers88012
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-81 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.205, 73.807, 154.659
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 8:37 or resseq 39:53 or (resid...
22(chain B and (resseq 8:10 or (resid 11 and (name...

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
111CCUUchain DDD9 - 239 - 23
211CCUUchain CCC9 - 239 - 23
112ARGARGGLNGLN(chain A and (resseq 8:37 or resseq 39:53 or (resid...AA8 - 378 - 37
122ASPASPVALVAL(chain A and (resseq 8:37 or resseq 39:53 or (resid...AA39 - 5339 - 53
132SERSERSERSER(chain A and (resseq 8:37 or resseq 39:53 or (resid...AA5454
142PHEPHEPHEPHE(chain A and (resseq 8:37 or resseq 39:53 or (resid...AA5555
152GLUGLUGLYGLY(chain A and (resseq 8:37 or resseq 39:53 or (resid...AA7 - 2527 - 252
212ARGARGPROPRO(chain B and (resseq 8:10 or (resid 11 and (name...BB8 - 108 - 10
222GLUGLUGLUGLU(chain B and (resseq 8:10 or (resid 11 and (name...BB1111
232ARGARGGLNGLN(chain B and (resseq 8:10 or (resid 11 and (name...BB8 - 2538 - 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: 28050.477 Da / Num. of mol.: 2 / Mutation: K155M
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, 144 molecules

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


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.87 Å3/Da / Density % sol: 61.2 %
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: Apr 20, 2017
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: 2.15→42.72 Å / Num. obs: 43520 / % possible obs: 96.7 % / Redundancy: 1 % / Biso Wilson estimate: 36.54 Å2 / Net I/σ(I): 10.8 / Num. measured all: 43520
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 1 % / Num. unique obs: 2988 / % possible all: 77.7

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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: 2.153→42.717 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.77
RfactorNum. reflection% reflection
Rfree0.2093 2130 4.91 %
Rwork0.1735 --
obs0.1752 43397 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.43 Å2 / Biso mean: 50.2534 Å2 / Biso min: 19.46 Å2
Refinement stepCycle: final / Resolution: 2.153→42.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 630 43 132 4585
Biso mean--75.45 48.77 -
Num. residues----519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074624
X-RAY DIFFRACTIONf_angle_d0.9486397
X-RAY DIFFRACTIONf_chiral_restr0.055757
X-RAY DIFFRACTIONf_plane_restr0.005714
X-RAY DIFFRACTIONf_dihedral_angle_d16.1572724
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D324X-RAY DIFFRACTION9.869TORSIONAL
12C324X-RAY DIFFRACTION9.869TORSIONAL
21A1975X-RAY DIFFRACTION9.869TORSIONAL
22B1975X-RAY DIFFRACTION9.869TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1532-2.20330.33591200.25412130225077
2.2033-2.25840.27821180.23522339245783
2.2584-2.31940.27681430.22792567271092
2.3194-2.38770.22681530.21482757291098
2.3877-2.46470.23391650.204927792944100
2.4647-2.55280.23021590.195928072966100
2.5528-2.6550.22781460.19328112957100
2.655-2.77580.25281510.195428182969100
2.7758-2.92210.27661640.202628002964100
2.9221-3.10520.23271320.196528733005100
3.1052-3.34480.22951340.17828462980100
3.3448-3.68130.2231210.162828833004100
3.6813-4.21350.1751240.149129093033100
4.2135-5.3070.14011270.130329393066100
5.307-42.7250.18611730.17173009318299
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)
13.56461.6875-1.38852.7945-1.38282.214-0.1702-0.2666-0.295-0.0355-0.0533-0.4160.13060.12550.24910.2585-0.00370.00130.1792-0.04560.25436.140.19745.0933
23.2952-0.7430.20984.5679-1.03585.0497-0.10740.47540.1932-0.7833-0.0847-0.3654-0.6258-0.12870.09670.4954-0.01620.01560.26610.00520.251421.96197.287836.0124
32.82550.2559-1.25161.6165-0.09422.1091-0.04460.15730.3565-0.17720.11370.1439-0.4234-0.2061-0.10930.38370.036-0.01270.24130.03240.308125.3149.469939.5078
42.6248-0.0385-1.34941.57520.35162.41680.0515-0.18710.23610.01060.1093-0.1115-0.09580.0384-0.15480.3436-0.0030.00130.19880.010.276630.6181.196443.4252
54.907-0.38050.63694.46230.45495.8815-0.04040.3664-0.1417-0.72280.1771-0.04030.27010.1441-0.13940.5357-0.01240.04860.2510.01370.31933.0253-14.926330.2734
63.521-0.04611.87571.749-0.20024.9892-0.0313-0.1444-0.0886-0.05680.03930.20750.2248-0.3820.00430.3169-0.00730.02990.16730.01630.242125.6208-9.297540.0903
76.9577-0.8381-0.83792.2076-3.05744.8434-0.56020.25160.8641-0.19080.3422-0.1284-1.231-0.48450.22180.63730.0591-0.17850.41820.03680.449516.33216.994231.1261
85.0608-3.5912-1.50944.28081.94243.5634-0.00830.0514-0.4065-0.1074-0.18710.63640.1616-0.42580.16430.3048-0.0463-0.04530.33070.06480.3586-0.88393.1595-10.2589
93.25310.1531-0.18582.4053-0.133.407-0.086-0.57360.37550.34910.2681-0.0352-0.15450.1672-0.20470.31920.0281-0.03530.3912-0.00020.270611.38699.9887-1.9916
103.4122-0.9202-0.1853.98740.10683.6513-0.1738-0.5055-0.61790.48380.1980.5270.6148-0.2241-0.02130.3542-0.0290.0340.33570.11220.35652.9686-6.3243-1.8855
112.03491.0112-0.06383.78213.60623.99890.0672-0.35840.17890.53340.1123-0.20540.19590.1825-0.260.43890.0919-0.10070.4825-0.00360.333419.43657.73125.408
121.23520.65152.17622.78160.19033.5677-0.09110.27510.0978-0.1610.02560.3689-0.4372-0.27540.03930.42530.04280.01780.49660.02610.339819.0879-0.819.5188
130.49410.15731.49751.4929-0.5133.7384-0.3136-0.02020.04080.19690.2421-0.0366-0.3899-0.1160.06320.38480.0481-0.02520.51360.04670.329114.8346-0.494416.0542
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 114 )A72 - 114
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 154 )A115 - 154
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 206 )A155 - 206
6X-RAY DIFFRACTION6chain 'A' and (resid 207 through 233 )A207 - 233
7X-RAY DIFFRACTION7chain 'A' and (resid 234 through 252 )A234 - 252
8X-RAY DIFFRACTION8chain 'B' and (resid 8 through 46 )B8 - 46
9X-RAY DIFFRACTION9chain 'B' and (resid 47 through 114 )B47 - 114
10X-RAY DIFFRACTION10chain 'B' and (resid 115 through 233 )B115 - 233
11X-RAY DIFFRACTION11chain 'B' and (resid 234 through 253 )B234 - 253
12X-RAY DIFFRACTION12chain 'C' and (resid 9 through 23 )C9 - 23
13X-RAY DIFFRACTION13chain 'D' and (resid 9 through 23 )D9 - 23

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