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

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Basic information

Entry
Database: PDB / ID: 6ozk
TitleCrystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after 68h soak in Ca2+
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: 2.104 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)70,63719
Polymers69,2044
Non-polymers1,43315
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-95 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.823, 73.012, 155.229
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 10:23)
21(chain C and resseq 10:23)
12(chain A and ((resid 7 and (name O or name...
22(chain B and (resseq 7:11 or resseq 13:14 or resseq...

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
111DIDIUU(chain D and resseq 10:23)DD10 - 2310 - 23
211DIDIUU(chain C and resseq 10:23)CC10 - 2310 - 23
112GLUGLUGLUGLU(chain A and ((resid 7 and (name O or name...AA72
122GLUGLUALAALA(chain A and ((resid 7 and (name O or name...AA7 - 2512 - 246
132GLUGLUALAALA(chain A and ((resid 7 and (name O or name...AA7 - 2512 - 246
142GLUGLUALAALA(chain A and ((resid 7 and (name O or name...AA7 - 2512 - 246
152GLUGLUALAALA(chain A and ((resid 7 and (name O or name...AA7 - 2512 - 246
212GLUGLUGLUGLU(chain B and (resseq 7:11 or resseq 13:14 or resseq...BB7 - 112 - 6
222THRTHRLEULEU(chain B and (resseq 7:11 or resseq 13:14 or resseq...BB13 - 148 - 9
232LEULEUALAALA(chain B and (resseq 7:11 or resseq 13:14 or resseq...BB16 - 2211 - 17
242LEULEUVALVAL(chain B and (resseq 7:11 or resseq 13:14 or resseq...BB24 - 5319 - 48
252ALAALAALAALA(chain B and (resseq 7:11 or resseq 13:14 or resseq...BB6 - 2511 - 246
262ALAALAALAALA(chain B and (resseq 7:11 or resseq 13:14 or resseq...BB6 - 2511 - 246
272ALAALAALAALA(chain B and (resseq 7:11 or resseq 13:14 or resseq...BB6 - 2511 - 246
282ALAALAALAALA(chain B and (resseq 7:11 or resseq 13:14 or resseq...BB6 - 2511 - 246
292ALAALAALAALA(chain B and (resseq 7:11 or resseq 13:14 or resseq...BB6 - 2511 - 246

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: 27308.598 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, 160 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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 4, 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→41.98 Å / Num. obs: 45195 / % possible obs: 93.8 % / Redundancy: 1 % / Biso Wilson estimate: 37.69 Å2 / Net I/σ(I): 10.5 / Num. measured all: 45195
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 1 % / Num. unique obs: 2689 / % possible all: 69

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.104→35.537 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.79 / Phase error: 24.56
RfactorNum. reflection% reflection
Rfree0.2143 4253 4.95 %
Rwork0.1768 --
obs0.1787 45111 93.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.13 Å2 / Biso mean: 54.8646 Å2 / Biso min: 26.31 Å2
Refinement stepCycle: final / Resolution: 2.104→35.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 630 88 145 4668
Biso mean--65.73 50.63 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074732
X-RAY DIFFRACTIONf_angle_d0.9726540
X-RAY DIFFRACTIONf_chiral_restr0.054769
X-RAY DIFFRACTIONf_plane_restr0.005734
X-RAY DIFFRACTIONf_dihedral_angle_d15.4212794
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D306X-RAY DIFFRACTION6.244TORSIONAL
12C306X-RAY DIFFRACTION6.244TORSIONAL
21A1934X-RAY DIFFRACTION6.244TORSIONAL
22B1934X-RAY DIFFRACTION6.244TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1038-2.12770.3544950.29491822191763
2.1277-2.15280.32191300.27962103223373
2.1528-2.1790.27621300.26712162229274
2.179-2.20660.30421090.25462296240580
2.2066-2.23560.24921090.25332308241779
2.2356-2.26620.27321110.23412390250182
2.2662-2.29860.25581380.2472489262786
2.2986-2.33290.28061400.25072667280792
2.3329-2.36940.28991500.24912713286395
2.3694-2.40820.29481370.23332828296598
2.4082-2.44970.28711400.21092936307699
2.4497-2.49420.23571650.20212841300699
2.4942-2.54220.23861330.19462886301999
2.5422-2.59410.21371540.187429073061100
2.5941-2.65050.20641710.188628763047100
2.6505-2.71210.18851380.193328893027100
2.7121-2.77990.27621000.20062952305299
2.7799-2.8550.25861440.214228923036100
2.855-2.9390.25051750.198928533028100
2.939-3.03380.24091310.202829173048100
3.0338-3.14220.22681610.183328583019100
3.1422-3.26790.22571530.18129153068100
3.2679-3.41650.21191280.174929253053100
3.4165-3.59650.18151650.16228663031100
3.5965-3.82160.1971650.160428853050100
3.8216-4.11630.20591560.149528813037100
4.1163-4.52970.18941550.132129193074100
4.5297-5.18350.16911110.133129333044100
5.1835-6.5240.18881630.167128793042100
6.524-35.54160.19011960.16112803299998
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)
18.13874.9179-3.91946.2519-3.44214.3054-0.2132-0.1175-0.3247-0.0984-0.0682-0.42710.20880.03440.2840.43210.03250.00730.19-0.08160.168436.50841.151444.6037
23.8028-0.0973-1.28751.2119-0.49082.4756-0.11230.36740.5916-0.43360.16290.0644-0.2841-0.2714-0.11020.587-0.0013-0.05470.30540.01310.318124.20139.311538.4723
34.9183-0.1401-1.83341.26880.12852.5272-0.02690.00430.3009-0.03670.0975-0.059-0.0078-0.1438-0.03320.48080.00880.01070.24260.01220.253130.58711.747343.6607
42.4095-0.71870.70142.88930.33662.7773-0.00840.2968-0.0552-0.59410.0192-0.00960.3433-0.1488-0.00820.6528-0.05950.01160.27230.02160.242727.8111-8.21633.5989
57.0191-3.6931-2.69946.85424.88117.3991-0.19560.1684-0.0926-0.1055-0.38730.91230.2061-0.59280.63660.4395-0.0547-0.03530.2910.07360.3988-0.75253.2429-10.0689
66.8146-2.3338-2.75157.4284.90843.5826-0.1648-0.71150.51390.74230.12190.05540.2018-0.06970.0510.58020.1087-0.04310.45380.00430.25212.81099.47571.0942
74.68431.8568-0.14342.95480.99013.6336-0.0672-0.47580.79880.37490.2203-0.1576-0.09690.4839-0.13470.60230.0379-0.07140.38770.05450.193311.86278.0592-1.8832
82.7363-1.01681.17043.58771.28492.47390.221-0.64290.90060.02530.095-0.0345-1.0650.3977-0.43530.55620.0161-0.09850.3426-0.03330.33629.331912.992-7.4153
99.08180.2698-2.72582.6560.15373.4713-0.0801-0.15210.17430.19380.06240.220.17170.01090.03990.44710.0192-0.02720.2439-0.00880.23414.72862.9851-8.4966
105.7281.0837-1.58044.1426-1.13196.2252-0.0864-0.5677-0.86661.06620.10560.62931.1496-0.2946-0.07591.0457-0.11120.21370.5290.09140.5231-0.6111-12.35514.4762
115.5563-2.47873.94526.8979-2.58247.1102-0.0107-0.228-0.3420.32280.0175-0.03650.77050.1449-0.04640.52010.00430.03540.28150.05230.24858.4067-7.5845-5.0918
123.81672.15352.27648.52987.27248.7831-0.12770.09250.39631.60380.0074-0.1729-0.11180.79420.05720.8323-0.0093-0.15740.5090.04140.343418.73697.03534.7353
133.88740.63053.9362.30360.35615.2647-0.24680.10710.3412-0.2481-0.06410.2738-0.1634-0.06160.30650.56570.0396-0.00330.3678-0.02080.314219.1052-0.158319.6137
141.9322-1.59893.2272.9124-2.13198.71390.0074-0.09450.2662-0.0219-0.0565-0.1483-0.2441-0.2841-0.03090.5364-0.0630.00130.37540.01120.299914.78520.022716.1388
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 114 )A47 - 114
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 154 )A115 - 154
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 251 )A155 - 251
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 46 )B6 - 46
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 71 )B47 - 71
7X-RAY DIFFRACTION7chain 'B' and (resid 72 through 95 )B72 - 95
8X-RAY DIFFRACTION8chain 'B' and (resid 96 through 114 )B96 - 114
9X-RAY DIFFRACTION9chain 'B' and (resid 115 through 154 )B115 - 154
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 206 )B155 - 206
11X-RAY DIFFRACTION11chain 'B' and (resid 207 through 233 )B207 - 233
12X-RAY DIFFRACTION12chain 'B' and (resid 234 through 251 )B234 - 251
13X-RAY DIFFRACTION13chain 'C' and (resid 9 through 23 )C9 - 23
14X-RAY DIFFRACTION14chain 'D' and (resid 9 through 23 )D9 - 23

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