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- PDB-6n6k: Human REXO2 bound to pAG -

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Basic information

Entry
Database: PDB / ID: 6n6k
TitleHuman REXO2 bound to pAG
Components
  • RNA (5'-R(P*AP*G)-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: 1.418 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*G)-3')
B: RNA exonuclease 2 homolog,Small fragment nuclease
C: RNA (5'-R(P*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9867
Polymers48,8374
Non-polymers1483
Water9,710539
1
A: RNA exonuclease 2 homolog,Small fragment nuclease
D: RNA (5'-R(P*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5444
Polymers24,4192
Non-polymers1252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-21 kcal/mol
Surface area10830 Å2
MethodPISA
2
B: RNA exonuclease 2 homolog,Small fragment nuclease
C: RNA (5'-R(P*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4423
Polymers24,4192
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-21 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.806, 87.423, 124.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA exonuclease 2 homolog,Small fragment nuclease / Oligoribonuclease / mitochondrial / 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 / 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*G)-3')


Mass: 629.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MLI / MALONATE ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
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: 1.418→45.806 Å / Num. all: 95286 / Num. obs: 95286 / % possible obs: 99.8 % / Redundancy: 7.8 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.078 / Rsym value: 0.073 / Net I/av σ(I): 7.1 / Net I/σ(I): 15.7 / Num. measured all: 746585
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.42-1.497.30.7241.1136420.2820.7790.72498.9
1.49-1.597.90.4731.6130500.1780.5060.473100
1.59-1.697.80.3092.5122590.1180.3310.309100
1.69-1.8380.2093.6114740.0790.2240.209100
1.83-2.0180.1345.5105390.0510.1440.134100
2.01-2.247.90.0838.695820.0320.0890.08399.9
2.24-2.598.10.0611185080.0230.0650.061100
2.59-3.177.90.04912.772490.0180.0520.049100
3.17-4.4880.03914.856830.0150.0410.039100
4.48-45.8067.50.03614.333000.0140.0390.03699.8

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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: 6N6A

6n6a


Resolution: 1.418→26.384 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.61
RfactorNum. reflection% reflection
Rfree0.1724 2372 2.49 %
Rwork0.1531 --
obs0.1536 95173 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.01 Å2 / Biso mean: 22.7865 Å2 / Biso min: 6.51 Å2
Refinement stepCycle: final / Resolution: 1.418→26.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 92 9 556 3746
Biso mean--55.54 36.31 -
Num. residues----385
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 (%)
1.4179-1.44680.26291360.25255250538697
1.4468-1.47830.22811360.212554435579100
1.4783-1.51270.19911380.19453545492100
1.5127-1.55050.22021400.180354025542100
1.5505-1.59240.19861380.172654385576100
1.5924-1.63930.15131390.16154265565100
1.6393-1.69220.18881360.157754025538100
1.6922-1.75260.15311400.154354295569100
1.7526-1.82280.17161380.150254365574100
1.8228-1.90570.14911400.151654355575100
1.9057-2.00620.17551400.155854485588100
2.0062-2.13180.18651370.148954405577100
2.1318-2.29630.18381410.150654895630100
2.2963-2.52720.19441400.15255025642100
2.5272-2.89260.1741420.155255225664100
2.8926-3.64280.17091420.138855675709100
3.6428-26.38830.13691490.139958185967100
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)
12.18920.52180.34432.01010.09130.740.03550.0160.0396-0.1077-0.00720.08220.0584-0.0378-0.03060.1046-0.00670.00220.1050.00130.0687-1.94358.213912.875
20.30580.2268-0.20152.0435-0.52950.56410.00870.01370.0032-0.12830.0036-0.05270.01910.0157-0.00990.0995-0.00180.00540.131-0.00550.10265.886118.160115.6036
30.9220.07872.75679.8212-1.2458.4740.24220.39590.1937-0.9056-0.4501-1.07110.18941.14350.23530.5863-0.010.0920.86930.02780.972933.32131.1899.0462
43.76580.91572.41694.2988-3.89266.47790.36561.97151.7312-1.5385-0.10580.4346-1.8656-0.8506-0.28070.55670.120.00450.43160.16480.5379-7.117943.131513.9836
51.062-0.1756-0.17780.82720.33680.7586-0.0166-0.1362-0.03340.1027-0.01120.04540.0672-0.05250.02680.0915-0.0154-0.00150.1186-0.00230.0938-3.810127.869832.3195
64.14050.056-2.41120.76441.07923.05570.0532-0.35290.14520.01050.0326-0.11-0.14810.4089-0.07350.0958-0.0057-0.01060.1128-0.02260.15389.545535.395328.8179
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 8:154)B8 - 154
6X-RAY DIFFRACTION6(chain B and resid 155:187)B155 - 187

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