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- PDB-8q66: Crystal Structure of the C. elegans MUT-7 MUT-8 CTD complex -

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Basic information

Entry
Database: PDB / ID: 8q66
TitleCrystal Structure of the C. elegans MUT-7 MUT-8 CTD complex
Components
  • Exonuclease mut-7
  • SH2 domain-containing protein
KeywordsRNA BINDING PROTEIN / small RNA amplification mutator complex exoribonuclease
Function / homology
Function and homology information


mutator focus / pre-miRNA 3'-end processing / 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing / post-transcriptional gene silencing / meiotic chromosome segregation / olfactory learning / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / associative learning / 3'-5' exonuclease activity ...mutator focus / pre-miRNA 3'-end processing / 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing / post-transcriptional gene silencing / meiotic chromosome segregation / olfactory learning / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / associative learning / 3'-5' exonuclease activity / nucleic acid binding / Hydrolases; Acting on ester bonds / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Mut7-C RNAse domain / Mut7-C RNAse domain / Exonuclease Mut-7, DEDDy 3'-5' exonuclease domain / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Exonuclease mut-7 / SH2 domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsFalk, S. / Busetto, V.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionFA743031European Union
CitationJournal: To Be Published
Title: MUT-7 a conserved exoribonuclease functioning in small RNA biogenesis
Authors: Falk, S. / Busetto, V.
History
DepositionAug 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exonuclease mut-7
B: SH2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4266
Polymers60,1742
Non-polymers2524
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-8 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.089, 59.053, 88.161
Angle α, β, γ (deg.)90.000, 119.800, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Exonuclease mut-7


Mass: 31667.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mut-7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): derivative / References: UniProt: P34607
#2: Protein SH2 domain-containing protein


Mass: 28506.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: rde-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): derivative / References: UniProt: Q19672
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 30 %w/v EDO_P8K (Precipitant) 0.1 M MB3 8.5 pH (Buffer) 0.06 M divalent (Complex ingredient)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.03→67.91 Å / Num. obs: 42083 / % possible obs: 99.73 % / Redundancy: 3.4 % / Biso Wilson estimate: 40.56 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08813 / Net I/σ(I): 9.1
Reflection shellResolution: 2.03→2.103 Å / Num. unique obs: 4152 / CC1/2: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.12.1-4487phasing
PHENIX1.12.1-4487refinement
PDB-REDOrefinement
pointlessdata scaling
XDS20230630data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→67.91 Å / SU ML: 0.3131 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 2109 5.01 %
Rwork0.1908 39974 -
obs0.1925 42083 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.42 Å2
Refinement stepCycle: LAST / Resolution: 2.03→67.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4155 0 13 250 4418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254277
X-RAY DIFFRACTIONf_angle_d0.56125795
X-RAY DIFFRACTIONf_chiral_restr0.0461642
X-RAY DIFFRACTIONf_plane_restr0.0149751
X-RAY DIFFRACTIONf_dihedral_angle_d6.191572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.070.37961410.38162582X-RAY DIFFRACTION96.9
2.07-2.130.36741470.32322646X-RAY DIFFRACTION99.93
2.13-2.180.28691350.29372650X-RAY DIFFRACTION99.82
2.18-2.250.30541470.27042646X-RAY DIFFRACTION99.75
2.25-2.320.29611300.25422643X-RAY DIFFRACTION99.64
2.32-2.40.29411470.23272668X-RAY DIFFRACTION99.93
2.4-2.50.27421290.23272683X-RAY DIFFRACTION99.93
2.5-2.610.27451360.23882650X-RAY DIFFRACTION99.75
2.61-2.750.30821430.22672644X-RAY DIFFRACTION99.61
2.75-2.920.26871560.21262666X-RAY DIFFRACTION99.89
2.92-3.150.23531460.18962669X-RAY DIFFRACTION99.96
3.15-3.470.22471150.1842708X-RAY DIFFRACTION99.86
3.47-3.970.18531430.15812679X-RAY DIFFRACTION99.68
3.97-50.16591560.13912674X-RAY DIFFRACTION99.51
5-67.910.18651380.16282766X-RAY DIFFRACTION99.35
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)
15.862293614860.9926415301943.71479839252.60430870135-0.7032843522476.054789193650.108876141223-0.1161220193690.334631282577-0.3387407763440.3623359995810.4263632481610.248589030195-0.296664845609-0.4884542294050.438115216218-0.102849952643-0.05866130018310.465833461489-0.1227758838370.65730731704522.2825969727-12.995503379222.4069043175
22.479564479651.50844471908-0.2575767190842.01703098582-0.7864241226564.57314145505-0.1923241168710.546230891059-0.593388474809-0.412895436890.132996412453-0.7560721622180.3892811828590.2796071399380.04865242082230.3450296119570.02720987095250.05969911285570.456758422259-0.1605537478710.51685763836343.4342934866-9.2854301379521.9349350928
32.48996798449-0.6071691517620.2157193705063.11339281134-0.4766366402432.780557191390.07186456358490.469239427880.136460928262-0.273766916794-0.0492235203139-0.127651057233-0.229567786847-0.0779234043142-0.01450257871520.2940169411690.002814324331640.03736010444730.4045156518820.01604196165730.33249657568532.85559441458.7633608244924.0989301223
40.9076402116890.205017092103-0.5845621178120.657100019692-0.7621421062962.70848836179-0.04882117128120.0986793277815-0.3121840002680.010265354582-0.0586794876277-0.1165822604480.231540027245-0.04910103359270.1066643704010.311925608136-0.00865488335657-0.02773428641250.286683390407-0.06646226298020.45038314768331.0306887282-13.236636572641.9267080731
51.67052083341-0.7098588558051.271386220673.024207018720.08389657639632.57983161189-0.112586778487-0.39390978814-0.3348820208890.4954605447760.1300048983230.03052758114960.462119397656-0.00404132540265-0.04258371303930.3397038823280.0358569532761-0.06284067868720.319981151660.06694360030510.45786348076133.4351141973-12.594567663261.233809723
62.605344030520.301549693249-0.04199109117591.266953982330.8793685308924.2016391225-0.01036391180550.121532102124-0.3713049082060.104125792803-0.04682603956270.02975813368910.363703370508-0.3641524610680.04525006408480.292747846849-0.021838945756-0.007724217142590.286317509983-0.03566385673880.39648038549729.120405063-10.798239548845.7598842201
72.331167497920.466890518932-0.143011761512.25620030733-0.1627864561454.041756116490.160741313542-0.1878707144160.222866645590.08311606132540.0221496327645-0.0335750098937-0.3745149138250.303194800045-0.1573437996750.291721113896-0.01194659926650.005858907376930.282869288027-0.05216275201160.41555898225439.36470540411.011791314156.2365556702
84.164558130120.8730767549630.03938229134282.774680394580.005717766421972.1464834578-0.004384573145470.1128233020220.198229177629-0.050175624105-0.02243173332930.341804897563-0.148491922064-0.4190819416350.02193226712660.3293462731910.05835015128240.00189725191150.3380517718780.01708804319330.30014267103217.49745434013.3070686706861.7405475094
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 628 through 641 )AA628 - 6411 - 14
22chain 'A' and (resid 642 through 661 )AA642 - 66115 - 34
33chain 'A' and (resid 662 through 735 )AA662 - 73535 - 108
44chain 'A' and (resid 736 through 831 )AA736 - 831109 - 204
55chain 'A' and (resid 832 through 846 )AA832 - 846205 - 219
66chain 'A' and (resid 847 through 898 )AA847 - 898220 - 271
77chain 'B' and (resid 326 through 446 )BF326 - 4461 - 121
88chain 'B' and (resid 447 through 567 )BF447 - 567122 - 242

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