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- PDB-4pmw: Structure of mouse Dis3L2 in complex with oligoU RNA substrate -

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Basic information

Entry
Database: PDB / ID: 4pmw
TitleStructure of mouse Dis3L2 in complex with oligoU RNA substrate
Components
  • DIS3-like exonuclease 2
  • U-U-U-U-U-U-U-U-U-U-U-U-U-U
KeywordsHydrolase/RNA / miRNA regulation / exonuclease / RNA Complex / RNA interference / Hydrolase-RNA complex
Function / homology
Function and homology information


polyuridylation-dependent mRNA catabolic process / miRNA catabolic process / exosome (RNase complex) / mitotic sister chromatid separation / : / poly(U) RNA binding / stem cell population maintenance / : / mRNA catabolic process / RNA nuclease activity ...polyuridylation-dependent mRNA catabolic process / miRNA catabolic process / exosome (RNase complex) / mitotic sister chromatid separation / : / poly(U) RNA binding / stem cell population maintenance / : / mRNA catabolic process / RNA nuclease activity / P-body / mitotic cell cycle / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / negative regulation of cell population proliferation / cell division / magnesium ion binding / cytoplasm
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #700 / DIS3-like exonuclease 2 / DIS3-like exonuclease 2, C-terminal / DIS3-like exonuclease 2 C terminal / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #700 / DIS3-like exonuclease 2 / DIS3-like exonuclease 2, C-terminal / DIS3-like exonuclease 2 C terminal / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain / RNB / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / DIS3-like exonuclease 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsFaehnle, C.R. / Walleshauser, J. / Joshua-Tor, L.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Louis Morin Charitable Trust United States
CitationJournal: Nature / Year: 2014
Title: Mechanism of Dis3l2 substrate recognition in the Lin28-let-7 pathway.
Authors: Faehnle, C.R. / Walleshauser, J. / Joshua-Tor, L.
History
DepositionMay 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Advisory / Author supporting evidence
Category: database_PDB_caveat / pdbx_struct_assembly_auth_evidence
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 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_struct_conn_angle / refine_hist / 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.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 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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: DIS3-like exonuclease 2
B: DIS3-like exonuclease 2
C: U-U-U-U-U-U-U-U-U-U-U-U-U-U
D: U-U-U-U-U-U-U-U-U-U-U-U-U-U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,7736
Polymers182,7244
Non-polymers492
Water1086
1
A: DIS3-like exonuclease 2
C: U-U-U-U-U-U-U-U-U-U-U-U-U-U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3863
Polymers91,3622
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-55 kcal/mol
Surface area33700 Å2
MethodPISA
2
B: DIS3-like exonuclease 2
D: U-U-U-U-U-U-U-U-U-U-U-U-U-U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3863
Polymers91,3622
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-58 kcal/mol
Surface area33760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.927, 96.075, 157.311
Angle α, β, γ (deg.)90.000, 98.750, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILELYSLYSchain AAA49 - 85613 - 770
21ILEILELYSLYSchain BBB49 - 85613 - 770
12UUUUchain CCC1 - 141 - 14
22UUUUchain DDD1 - 141 - 14

NCS ensembles :
ID
1
2
DetailsGel filtration confirms 1 protein polymer and 1 RNA polymer make up the biological unit in solution

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Components

#1: Protein DIS3-like exonuclease 2


Mass: 87120.766 Da / Num. of mol.: 2 / Mutation: D389N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dis3l2 / Plasmid: Multi-Bac pFL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q8CI75, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: RNA chain U-U-U-U-U-U-U-U-U-U-U-U-U-U


Mass: 4241.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.61 Å3/Da / Density % sol: 52.9 % / Description: plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM ammonium citrate pH 5.5, 200 mM ammonium chloride, 22 % PEG 3350
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.95→96.1 Å / Num. obs: 39795 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.08 / Net I/σ(I): 8 / Num. measured all: 136961
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
2.95-3.33.50.4632.939093112650.2999.9
6.6-96.073.40.06316.31226536540.0499.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata scaling
SCALAdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
XSCALEdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→63.182 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 2000 5.03 %Random selection
Rwork0.2021 37754 --
obs0.2046 39754 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.96 Å2 / Biso mean: 78.5518 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.95→63.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11016 560 2 6 11584
Biso mean--44.71 30.82 -
Num. residues----1410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211862
X-RAY DIFFRACTIONf_angle_d0.95716170
X-RAY DIFFRACTIONf_chiral_restr0.0291862
X-RAY DIFFRACTIONf_plane_restr0.0041994
X-RAY DIFFRACTIONf_dihedral_angle_d12.834600
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8514X-RAY DIFFRACTION6.939TORSIONAL
12B8514X-RAY DIFFRACTION6.939TORSIONAL
21C360X-RAY DIFFRACTION6.939TORSIONAL
22D360X-RAY DIFFRACTION6.939TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9504-3.02420.37011470.311227162863100
3.0242-3.1060.31291380.294426582796100
3.106-3.19740.33471380.277827032841100
3.1974-3.30060.33381450.263426552800100
3.3006-3.41850.28441550.256426722827100
3.4185-3.55540.28851470.235627062853100
3.5554-3.71720.31671290.210326822811100
3.7172-3.91310.21911230.199126862809100
3.9131-4.15820.24641480.19127082856100
4.1582-4.47920.21211470.170326722819100
4.4792-4.92980.2081360.155427182854100
4.9298-5.64280.23131600.17226962856100
5.6428-7.10780.21411520.196627122864100
7.1078-63.19690.21521350.17322770290599
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)
13.9994-1.3979-0.57742.20640.11261.4636-0.2708-0.5296-0.08560.20120.4171-0.317-0.14120.4964-0.14320.47130.0097-0.06460.5386-0.09740.47659.219643.145599.2409
21.0018-0.0147-0.41721.55480.11063.1552-0.0331-0.0502-0.09480.03750.0543-0.08690.22460.2722-0.01220.37360.05170.04230.3294-0.04870.3596-2.925424.171877.7537
31.4939-0.0472-1.70563.44673.93196.3037-0.0406-0.7097-0.11081.360.18190.01851.16260.9439-0.14010.88010.16520.10660.77750.00560.65351.26926.172393.3117
41.311-0.56931.29633.65612.55334.12440.09460.3580.4681-0.80730.2454-0.3632-1.0131.0062-0.30151.0173-0.1008-0.04040.6375-0.01660.582616.601655.8923-11.2257
54.48920.7287-0.52322.99040.47012.4953-0.421-0.0530.14230.10780.5396-0.68610.18940.6768-0.14240.64550.07370.01310.5308-0.12350.617126.897739.768-14.5274
61.32640.1509-0.53332.02360.33132.8570.1214-0.18410.08840.2419-0.03640.0628-0.04590.2023-0.08850.63510.00780.01760.3474-0.06580.3577.78956.80110.8897
72.0133-0.91752.34651.4444-2.41916.56940.08840.45690.1347-0.321-0.0435-0.1123-0.16110.5333-0.01680.85210.04610.10210.4698-0.06210.40418.260260.1828-22.2748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 352 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 353 through 856 )A0
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 14 )C0
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 14 )D0
5X-RAY DIFFRACTION5chain 'B' and (resid 49 through 352 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 353 through 728 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 729 through 856 )B0

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