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- PDB-6sty: Human REXO2 exonuclease in complex with RNA. -

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Basic information

Entry
Database: PDB / ID: 6sty
TitleHuman REXO2 exonuclease in complex with RNA.
Components
  • Oligoribonuclease, mitochondrial
  • RNA (5'-R(P*AP*UP*C)-3')
KeywordsRNA BINDING PROTEIN / 3'-5' exonuclease in complex with its RNA substrate
Function / homology
Function and homology information


Mitochondrial RNA degradation / Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix ...Mitochondrial RNA degradation / Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix / focal adhesion / nucleolus / magnesium ion binding / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Oligoribonuclease / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Oligoribonuclease, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsMalik, D. / Szewczyk, M. / Szczesny, R. / Nowotny, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2014/12/W/NZ1/00463 Poland
Citation
Journal: Nucleic Acids Res. / Year: 2020
Title: Human REXO2 controls short mitochondrial RNAs generated by mtRNA processing and decay machinery to prevent accumulation of double-stranded RNA.
Authors: Szewczyk, M. / Malik, D. / Borowski, L.S. / Czarnomska, S.D. / Kotrys, A.V. / Klosowska-Kosicka, K. / Nowotny, M. / Szczesny, R.J.
#1: Journal: Nucleic Acids Res. / Year: 2001
Title: Exoribonuclease superfamilies: structural analysis and phylogenetic distribution.
Authors: Zuo, Y. / Deutscher, M.P.
History
DepositionSep 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Oligoribonuclease, mitochondrial
B: Oligoribonuclease, mitochondrial
C: RNA (5'-R(P*AP*UP*C)-3')
D: Oligoribonuclease, mitochondrial
E: Oligoribonuclease, mitochondrial
F: RNA (5'-R(P*AP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3727
Polymers114,3316
Non-polymers401
Water1629
1
A: Oligoribonuclease, mitochondrial
B: Oligoribonuclease, mitochondrial
C: RNA (5'-R(P*AP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2064
Polymers57,1663
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-31 kcal/mol
Surface area17930 Å2
MethodPISA
2
D: Oligoribonuclease, mitochondrial
E: Oligoribonuclease, mitochondrial
F: RNA (5'-R(P*AP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)57,1663
Polymers57,1663
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-21 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.303, 88.303, 123.773
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein
Oligoribonuclease, mitochondrial / RNA exonuclease 2 homolog / Small fragment nuclease


Mass: 26873.824 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REXO2, SFN, SMFN, CGI-114 / Plasmid: pET28 SUMO
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Y3B8, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*AP*UP*C)-3')


Mass: 3418.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M potassium sodium tartrate trihydrate and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.8944 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8944 Å / Relative weight: 1
ReflectionResolution: 3.15→48.11 Å / Num. obs: 18669 / % possible obs: 99.4 % / Redundancy: 5.1 % / CC1/2: 0.994 / Net I/σ(I): 14.81
Reflection shellResolution: 3.15→3.34 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.06 / Num. unique obs: 2940 / CC1/2: 0.828 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CY4

5cy4


Resolution: 3.15→48.11 Å / Cross valid method: FREE R-VALUE / σ(F): 176.47 / Phase error: 21.3428
RfactorNum. reflection% reflection
Rfree0.2217 933 5.01 %
Rwork0.1629 --
obs0.1988 18629 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 84.02 Å2
Refinement stepCycle: LAST / Resolution: 3.15→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5907 93 1 9 6010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256141
X-RAY DIFFRACTIONf_angle_d0.53128346
X-RAY DIFFRACTIONf_chiral_restr0.0378939
X-RAY DIFFRACTIONf_plane_restr0.00321072
X-RAY DIFFRACTIONf_dihedral_angle_d11.66064072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.320.35391330.2632516X-RAY DIFFRACTION94.55
3.32-3.520.26421330.21852534X-RAY DIFFRACTION94.98
3.52-3.80.26971330.20042520X-RAY DIFFRACTION94.99
3.8-4.180.25771330.18852518X-RAY DIFFRACTION94.88
4.18-4.780.23511330.1792543X-RAY DIFFRACTION94.99
4.78-6.020.21841330.17822524X-RAY DIFFRACTION94.99
6.02-48.110.24661340.20372534X-RAY DIFFRACTION94.84
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)
13.73501050084-1.19856272787-3.872260213513.392941745490.1032445134294.443380800590.854851840946-0.07235808130041.313560026430.2704217696270.7569595844232.019493591310.2027402386730.924979243374-1.680745300411.362037526440.2977390550970.3096512813271.021844745550.1347590297090.990269386034-5.2498405610718.2201262393-6.38769400297
24.212926815481.693754931912.970307105942.994173020321.655954059292.366394268670.1448217990.01712699902980.241740281160.529983122098-0.58645712780.2652075895510.8111081504180.09110294861980.3166475942560.633026052614-0.1119815198670.06744938795360.6215639446150.06434684116590.35664721489-0.282248938609-48.1952179295-34.8459449161
32.687017471710.779739279007-0.6323772834092.845177060950.8053630243742.910539308250.367670991356-0.1250684093470.2362173316550.17819755159-0.329007945341-0.0952918776059-0.8019681738220.329145264792-0.02559418815090.881025313337-0.1039952618350.1073494023770.57422841870.06837355519820.4132051159382.75502802875-38.5449262838-20.197333537
42.25644972-0.894944722579-0.7794661240945.87672295894-1.306074813885.376839955740.248696693444-0.125793266357-0.2341976855030.0156628773715-0.455504348639-0.4108637466040.1572195897670.6609118268890.2231415053370.4716738550340.03477548094850.01207424035370.6158626070760.07952792401820.4378166168023.58068760216-57.9997327714-22.9114164525
59.20667759922-3.99929835535-2.089404344257.007444679121.433601416644.404838889880.4490691059350.471107752723-0.1354833797420.238274453679-0.603924547660.422393291093-0.429648983589-0.4373624346970.1472374169240.537318348632-0.1180001102680.0017584275080.5239591076070.04357326974330.429218087676-17.6584305521-57.641502372-12.3467165607
69.6205797901-4.141315507396.614158573256.51108789613-3.399507078534.866149735670.1268154290720.8493954630471.1287815753-0.17327858847-0.2897977952390.250673706048-1.46593333955-1.574694541920.0595693103061.113133906710.3744231966910.2118551174631.295413084970.1855688839781.17620246636-30.9307561949-42.7958010483-21.675654328
77.92530768049-1.901448827926.588730346661.37431317256-2.547040906276.601161212720.2572128221440.4923207276870.15512746653-0.2543790259860.07482191855071.421024936120.13306803454-1.90022061233-0.1293448000950.6835812519030.101758779061-0.03223562048351.05507240348-0.05812311756611.21752490501-34.8412044188-48.4844152716-14.1686768735
83.4996850531-3.74297158921-2.845791805986.290945018390.02634820547556.323981409020.225111033579-0.351832985850.2895626184910.489467325715-0.1825008498530.187750652038-0.65420150924-0.323524872182-0.2664061098520.654031293193-0.107326110766-0.01283813727320.627033943598-0.05033238596550.466692309968-17.5252928724-55.8436435516-4.96161667984
96.364427030130.0270404093062-4.394289133332.546410832920.7558520932593.26151351451.00836202238-0.7570226072960.6291430771950.1535693961750.08623628990080.0521091700109-1.509436661110.386928617618-0.9992429761580.785944837316-0.08066619752860.1190526064410.68062292436-0.1193925758250.526845776572-12.6229385817-49.4477336044-10.0173252496
106.168693931921.2102769504-2.693360149345.970336968690.3410854449019.189337554330.05434536776390.9657278355-0.762928607885-1.261219518260.1627679131770.5525990446530.855652699365-0.982875287044-0.1280625080280.849121830312-0.0650446075372-0.09482625376380.67646996532-0.1117477320190.468081272707-10.1493380959-64.1471511787-27.0567810096
112.869969630660.763047541877-3.850390323546.684539052473.203301026517.93743023955-1.29100577514-2.802491924021.024808897134.890953890040.5018955806064.603804431350.104902180889-2.905421564090.6972675652671.704525185220.6318640734090.2427888425092.69630110087-0.4781573174891.8060487279-19.3439208112-50.5904828161-24.413430593
122.59470512240.1509450103651.681862653260.755495034668-1.065442832798.615595020260.0627114536792-0.361016302081-0.109939063588-0.24086944616-0.281954555651-0.305015895530.476173432877-0.6928055579110.1753531463610.4504352599660.01162088384080.08389937894270.444576503756-0.03435806690080.3968237681117.10708707627-0.308363046192-7.59100279693
138.657747497052.52451757661-1.880173835799.701766627930.066743105478.876355216220.05835751365540.335954457185-0.7495358712991.125842960520.179328983125-0.7461606919790.2175213183920.895036515953-0.1808105266610.5689881671510.0501535389721-0.1836383813350.602064439864-0.08483590600010.67620465680218.757115338-2.0495550819512.0880218807
145.026269533420.5838294036282.118255647681.99754566264-0.5032321593384.45412413648-0.2907597638470.6688481575110.366458463295-0.04936478186740.095550047186-0.341175985082-0.4250531393250.4394359263340.1975593898450.570267346475-0.1419966735810.06582542502610.646794328791-0.1518487914080.46710660430512.00067442453.57656571421-9.54469086031
152.125377202032.610103417112.491639369996.432676616781.780246950438.812832535860.08666003552950.03042214774460.157681250103-0.3009755563490.350410592758-0.391544655706-0.5069604274610.372217933591-0.3949630368030.46862630784-0.02997704022770.03886336227170.4428467025740.02588932642080.4443182579797.085610367418.74608233156-2.64672327295
167.75283049585-0.560363592705-1.273931601072.8595763561.448283228493.97206277713-0.394883303086-0.618226019812-0.6952279532650.1579566150590.07549468783890.02119388962170.778530550562-0.1607951922760.2507634501180.7014302635580.01083405009450.05250017066160.473125595931-0.0157529533270.416646346982-5.58277080279-8.873103008680.641763286139
174.290301397-2.85736250405-3.726056695182.737831160393.253544803144.004352337780.3447258386030.8160603135910.5310921191710.0738584454653-0.7952727111920.4771306183180.661773764183-0.6682627407370.2245275440440.799397402409-0.2031247213070.1256362166881.00892135086-0.1010355769710.419837413806-17.7022057992-13.6369680543-14.972654744
184.059199484252.57278843583-0.2759441424637.21303298263-0.1584419204082.90674846842-0.3972979451730.0087214890197-0.0445415817132-0.2525043178680.370652727457-0.265324728318-0.404020228151-0.5609968386250.03623777958040.6254855475130.167120650566-0.04091973129170.643566257126-0.087980258590.348636330612-12.517636074312.26370400578.23542663392
192.746314342220.465242711734-2.2138711714.7527350363-2.938353507793.206773766990.2359274151230.3180978535441.33543271839-1.21407062302-0.0941530039543-1.00045037754-0.126812785546-0.0227568583588-0.02754299187891.39842207141-0.01549789013880.09205883537860.8235775882520.009442819320350.787358682031-2.3081549353230.7800528691-1.64827956711
202.652265120981.51081693231-1.051814268627.89748082864-1.686199612291.86616914884-0.00414004036354-0.2626828807880.5285644676850.664346616847-0.07002330887910.0806818674923-0.897713505548-0.3190006551750.08319469530730.820881051280.195135116213-0.1170724483240.656689686494-0.1159332964690.458610825305-10.337354161419.625138061112.2691920008
213.57835340990.356817816820.07815587485643.372086654362.998507003446.304596103550.06612697528890.3705546104450.306170776563-0.0834409784754-0.0144424273291-0.0505684757323-0.192686523727-0.659415916281-0.07126120895050.6083772952870.0757241175822-0.04607720098110.537894884235-0.001836464907150.343783686569-11.25094852077.6848027389-1.64673384317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 0 through 2 )
2X-RAY DIFFRACTION2chain 'D' and (resid 28 through 50 )
3X-RAY DIFFRACTION3chain 'D' and (resid 51 through 154 )
4X-RAY DIFFRACTION4chain 'D' and (resid 155 through 227 )
5X-RAY DIFFRACTION5chain 'E' and (resid 34 through 82 )
6X-RAY DIFFRACTION6chain 'E' and (resid 83 through 103 )
7X-RAY DIFFRACTION7chain 'E' and (resid 104 through 116 )
8X-RAY DIFFRACTION8chain 'E' and (resid 117 through 143 )
9X-RAY DIFFRACTION9chain 'E' and (resid 144 through 165 )
10X-RAY DIFFRACTION10chain 'E' and (resid 166 through 218 )
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 2 )
12X-RAY DIFFRACTION12chain 'A' and (resid 28 through 82 )
13X-RAY DIFFRACTION13chain 'A' and (resid 83 through 116 )
14X-RAY DIFFRACTION14chain 'A' and (resid 117 through 143 )
15X-RAY DIFFRACTION15chain 'A' and (resid 144 through 165 )
16X-RAY DIFFRACTION16chain 'A' and (resid 166 through 214 )
17X-RAY DIFFRACTION17chain 'A' and (resid 215 through 228 )
18X-RAY DIFFRACTION18chain 'B' and (resid 30 through 82 )
19X-RAY DIFFRACTION19chain 'B' and (resid 83 through 104 )
20X-RAY DIFFRACTION20chain 'B' and (resid 105 through 143 )
21X-RAY DIFFRACTION21chain 'B' and (resid 144 through 219 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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