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- PDB-6n6j: Human REXO2 bound to pAA -

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Basic information

Entry
Database: PDB / ID: 6n6j
TitleHuman REXO2 bound to pAA
Components
  • RNA (5'-R(P*AP*A)-3')
  • RNA exonuclease 2 homolog,Small fragment nuclease
Keywordsrna binding protein/rna / 3'-5' exoribonuclease / RNA BINDING PROTEIN / rna binding protein-rna complex
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-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / RNA / Oligoribonuclease, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.317 Å
AuthorsLormand, J.D. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123609 United States
CitationJournal: Elife / Year: 2019
Title: A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation.
Authors: Kim, S.K. / Lormand, J.D. / Weiss, C.A. / Eger, K.A. / Turdiev, H. / Turdiev, A. / Winkler, W.C. / Sondermann, H. / Lee, V.T.
History
DepositionNov 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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 / 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_alt_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_alt_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_ptnr1_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA exonuclease 2 homolog,Small fragment nuclease
D: RNA (5'-R(P*AP*A)-3')
B: RNA exonuclease 2 homolog,Small fragment nuclease
C: RNA (5'-R(P*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,20010
Polymers48,8054
Non-polymers3946
Water8,197455
1
A: RNA exonuclease 2 homolog,Small fragment nuclease
D: RNA (5'-R(P*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6205
Polymers24,4032
Non-polymers2173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-23 kcal/mol
Surface area10770 Å2
MethodPISA
2
B: RNA exonuclease 2 homolog,Small fragment nuclease
C: RNA (5'-R(P*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5805
Polymers24,4032
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-18 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.863, 87.566, 124.225
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain , 2 types, 4 molecules ABDC

#1: Protein RNA exonuclease 2 homolog,Small fragment nuclease / REXO2


Mass: 23789.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REXO2, SFN, SMFN, CGI-114 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q9Y3B8, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*AP*A)-3')


Mass: 613.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 461 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M sodium malonate (pH 5.5) and 15-20% polyethylene glycol 3350, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2018
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.317→45.863 Å / Num. obs: 118674 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.068 / Rsym value: 0.063 / Net I/av σ(I): 7.9 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.32-1.394.50.6341.2167270.3290.7180.63497.4
1.39-1.4770.4681.7163150.1910.5070.468100
1.47-1.5780.2922.6153320.1110.3130.292100
1.57-1.77.90.1864.1143130.0710.20.186100
1.7-1.8680.1236.1131870.0460.1320.123100
1.86-2.0880.0789.2119900.030.0840.078100
2.08-2.48.10.05712.3106010.0210.0610.057100
2.4-2.9480.04614.390260.0170.0490.046100
2.94-4.167.70.03715.871090.0140.040.037100
4.16-45.8637.60.03415.740740.0130.0370.03499.8

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N6I

6n6i


Resolution: 1.317→31.669 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.97
RfactorNum. reflection% reflection
Rfree0.1701 2958 2.5 %
Rwork0.1528 --
obs0.1533 118555 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.3 Å2 / Biso mean: 19.686 Å2 / Biso min: 5.5 Å2
Refinement stepCycle: final / Resolution: 1.317→31.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 90 29 495 3703
Biso mean--33.95 32.81 -
Num. residues----385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3167-1.33830.32221280.28165013514192
1.3383-1.36130.24221400.243554505590100
1.3613-1.38610.24151400.212154895629100
1.3861-1.41280.20751390.198654485587100
1.4128-1.44160.19881410.184354855626100
1.4416-1.47290.16821400.170854665606100
1.4729-1.50720.16731390.1654725611100
1.5072-1.54490.1681400.150854965636100
1.5449-1.58670.16641400.149654805620100
1.5867-1.63340.1461410.147354735614100
1.6334-1.68610.16911410.145754805621100
1.6861-1.74630.14221410.145255025643100
1.7463-1.81620.15341410.147355025643100
1.8162-1.89890.15961400.143455325672100
1.8989-1.9990.17891430.146455025645100
1.999-2.12420.14871410.141755325673100
2.1242-2.28820.14641420.141355735715100
2.2882-2.51840.16111430.148355575700100
2.5184-2.88260.19691430.156456265769100
2.8826-3.63090.16611460.140656475793100
3.6309-31.67820.16491490.148958726021100
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)
12.04330.56580.49131.73620.16940.67130.014-0.00640.0042-0.09740.00450.05790.0371-0.0312-0.02980.0923-0.00410.00240.09010.0020.0611-1.57388.18312.6855
20.3050.1798-0.17721.723-0.47850.56620.01290.0194-0.0056-0.1204-0.0074-0.04530.020.0072-0.00330.09160.00120.0030.1196-0.00270.09875.987318.044715.7413
38.5667-2.11985.13867.309-0.83793.10990.51360.89440.0756-1.1788-0.3998-1.0394-0.01121.0186-0.10720.54290.04130.1250.73710.04380.61933.500931.21639.088
43.74052.65922.09795.2706-2.30585.44650.23252.05141.7648-1.4203-0.11140.2852-1.9271-0.7241-0.16090.52370.1065-0.00040.390.17660.4514-6.98443.225614.0536
50.9417-0.1776-0.10351.14230.10031.1278-0.0112-0.1203-0.05450.11-0.01750.08920.0973-0.09660.01790.0797-0.01760.00690.1116-0.00530.0967-6.675827.840733.7716
63.0271-0.2904-1.51820.81360.54621.24360.0069-0.19450.1354-0.00560.0689-0.1059-0.07520.205-0.06160.0809-0.0146-0.01160.0999-0.01380.109612.576132.562126.9073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:86)A4 - 86
2X-RAY DIFFRACTION2(chain A and resid 87:184)A87 - 184
3X-RAY DIFFRACTION3(chain A and resid 185:198)A185 - 198
4X-RAY DIFFRACTION4(chain B and resid 2:7)B2 - 7
5X-RAY DIFFRACTION5(chain B and resid 8:137)B8 - 137
6X-RAY DIFFRACTION6(chain B and resid 138:187)B138 - 187

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