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- PDB-6f4a: Yeast mitochondrial RNA degradosome complex mtEXO -

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Basic information

Entry
Database: PDB / ID: 6f4a
TitleYeast mitochondrial RNA degradosome complex mtEXO
Components
  • Exoribonuclease II, mitochondrial
  • RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3')
  • Suv3 helicase
KeywordsHYDROLASE / RNA degradation / mitochondria / nuclease / helicase / protein complex
Function / homology
Function and homology information


mitochondrial degradosome / hydrolase activity, acting on acid anhydrides / exoribonuclease II activity / mitochondrial RNA catabolic process / mitochondrial chromosome / mitochondrial DNA replication / mRNA catabolic process / Group I intron splicing / RNA nuclease activity / P-body ...mitochondrial degradosome / hydrolase activity, acting on acid anhydrides / exoribonuclease II activity / mitochondrial RNA catabolic process / mitochondrial chromosome / mitochondrial DNA replication / mRNA catabolic process / Group I intron splicing / RNA nuclease activity / P-body / RNA helicase activity / RNA helicase / mitochondrion / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Mitochondrial degradasome RNA helicase subunit, C-terminal domain / Suv3, DEXQ-box helicase domain / ATP-dependent RNA helicase SUV3 C-terminal domain / DEXQ-box helicase domain of Suv3 / : / Ribonuclease II/R / RNB domain / RNB / : / Helicase conserved C-terminal domain ...Mitochondrial degradasome RNA helicase subunit, C-terminal domain / Suv3, DEXQ-box helicase domain / ATP-dependent RNA helicase SUV3 C-terminal domain / DEXQ-box helicase domain of Suv3 / : / Ribonuclease II/R / RNB domain / RNB / : / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Exoribonuclease II, mitochondrial / Candida glabrata strain CBS138 chromosome M complete sequence / RNA helicase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsRazew, M. / Nowak, E. / Nowotny, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre Poland00463 Poland
CitationJournal: Nat Commun / Year: 2018
Title: Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components.
Authors: Razew, M. / Warkocki, Z. / Taube, M. / Kolondra, A. / Czarnocki-Cieciura, M. / Nowak, E. / Labedzka-Dmoch, K. / Kawinska, A. / Piatkowski, J. / Golik, P. / Kozak, M. / Dziembowski, A. / Nowotny, M.
History
DepositionNov 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exoribonuclease II, mitochondrial
B: Suv3 helicase
C: RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)170,0643
Polymers170,0643
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-29 kcal/mol
Surface area62780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.550, 151.240, 284.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Exoribonuclease II, mitochondrial


Mass: 94687.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 69 aminoacid N-terminal truncation was introduced in the full length protein
Source: (gene. exp.) Candida glabrata (fungus) / Gene: AO440_004157 / Production host: Escherichia coli (E. coli) / Variant (production host): RIL / References: UniProt: A0A0W0CXR7, UniProt: Q6FJE0*PLUS
#2: Protein Suv3 helicase


Mass: 73477.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 42 aminoacid N-terminal truncation and 14 aminoacid C-terminal truncation was introduced to the full length protein
Source: (gene. exp.) Candida glabrata (fungus) / Gene: SUV3, CAGL0L12386g / Production host: Escherichia coli (E. coli) / Variant (production host): RIL / References: UniProt: Q6FKD7
#3: RNA chain RNA (5'-R(P*AP*GP*AP*UP*AP*C)-3')


Mass: 1899.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RNA molecule co-purified with the protein / Source: (natural) Escherichia coli (E. coli) / Variant: RIL

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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: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium citrate tribasic (pH 7.0), 18% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.55→50.1 Å / Num. obs: 26391 / % possible obs: 95.4 % / Redundancy: 4.3 % / Rrim(I) all: 0.033 / Net I/σ(I): 27.4
Reflection shellResolution: 3.55→3.64 Å / Rrim(I) all: 0.225

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F3H, 3RC3

6f3h

3rc3


Resolution: 3.55→49.061 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 37.64 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3279 1318 4.99 %
Rwork0.2963 --
obs0.2978 26391 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.55→49.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7455 119 0 0 7574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077698
X-RAY DIFFRACTIONf_angle_d1.4410604
X-RAY DIFFRACTIONf_dihedral_angle_d12.4522243
X-RAY DIFFRACTIONf_chiral_restr0.0511319
X-RAY DIFFRACTIONf_plane_restr0.0081387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.55-3.69210.37531740.33962750X-RAY DIFFRACTION96
3.6921-3.86010.41761420.3412802X-RAY DIFFRACTION98
3.8601-4.06350.41281560.33922772X-RAY DIFFRACTION97
4.0635-4.3180.3211530.30562801X-RAY DIFFRACTION97
4.318-4.65110.33321510.28292741X-RAY DIFFRACTION95
4.6511-5.11870.36731360.28942846X-RAY DIFFRACTION97
5.1187-5.85840.35821260.33252756X-RAY DIFFRACTION94
5.8584-7.37690.35811390.32242806X-RAY DIFFRACTION95
7.3769-49.06560.2661410.25992799X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -3.4509 Å / Origin y: -51.2107 Å / Origin z: 31.8815 Å
111213212223313233
T1.1636 Å2-0.2299 Å20.0002 Å2-0.8711 Å20.0306 Å2--0.8244 Å2
L2.4411 °2-0.4305 °20.6347 °2-0.4778 °20.0311 °2--1.8229 °2
S0.1075 Å °-0.6573 Å °0.2265 Å °-0.1936 Å °-0.0294 Å °-0.1253 Å °-0.6751 Å °0.1983 Å °-0.074 Å °
Refinement TLS groupSelection details: all

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