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- PDB-4db4: Mss116p DEAD-box helicase domain 2 bound to a chimaeric RNA-DNA duplex -

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Basic information

Entry
Database: PDB / ID: 4db4
TitleMss116p DEAD-box helicase domain 2 bound to a chimaeric RNA-DNA duplex
Components
  • 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
  • ATP-dependent RNA helicase MSS116, mitochondrial
KeywordsRNA-BINDING PROTEIN/DNA / RNA / DEAD-box / RNA helicase / hydrolase / RNA-BINDING PROTEIN-DNA / RNA complex
Function / homology
Function and homology information


Group II intron splicing / transcription elongation by mitochondrial RNA polymerase / mitochondrial RNA processing / mitochondrial translational initiation / RNA strand annealing activity / G-quadruplex DNA binding / mitochondrial translational elongation / mitochondrial ribosome / Group I intron splicing / RNA folding ...Group II intron splicing / transcription elongation by mitochondrial RNA polymerase / mitochondrial RNA processing / mitochondrial translational initiation / RNA strand annealing activity / G-quadruplex DNA binding / mitochondrial translational elongation / mitochondrial ribosome / Group I intron splicing / RNA folding / mRNA processing / regulation of translation / G-quadruplex RNA binding / RNA helicase activity / RNA helicase / mitochondrial matrix / mRNA binding / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 ...DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA/RNA hybrid / DNA/RNA hybrid (> 10) / ATP-dependent RNA helicase MSS116, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.599 Å
AuthorsMallam, A.L. / Del Campo, M. / Gilman, B.D. / Sidote, D.J. / Lambowitz, A.
CitationJournal: Nature / Year: 2012
Title: Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p.
Authors: Mallam, A.L. / Del Campo, M. / Gilman, B. / Sidote, D.J. / Lambowitz, A.M.
History
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Oct 10, 2012Group: Database references / Derived calculations
Revision 1.3Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase MSS116, mitochondrial
B: ATP-dependent RNA helicase MSS116, mitochondrial
C: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
D: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
E: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
F: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)75,8386
Polymers75,8386
Non-polymers00
Water00
1
A: ATP-dependent RNA helicase MSS116, mitochondrial
C: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
D: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
E: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
F: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)46,7115
Polymers46,7115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase MSS116, mitochondrial

C: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
D: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
E: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'
F: 5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)46,7115
Polymers46,7115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Unit cell
Length a, b, c (Å)43.696, 70.112, 214.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
32E
42F
13C
23D
33E
43F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 341:596 ) and (not element H)A0
211chain 'B' and (resseq 341:596 ) and (not element H)B0
112chain 'C' and (resseq -1:6 ) and (not element H)C0
212chain 'D' and (resseq 13:20 ) and (not element H)D0
312chain 'E' and (resseq 13:20 ) and (not element H)E0
412chain 'F' and (resseq -1:6 ) and (not element H)F0
113chain 'C' and (resseq -6:-2 ) and (not element H)C0
213chain 'D' and (resseq 8:12 ) and (not element H)D0
313chain 'E' and (resseq 8:12 ) and (not element H)E0
413chain 'F' and (resseq -6:-2 ) and (not element H)F0

NCS ensembles :
ID
1
2
3

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Components

#1: Protein ATP-dependent RNA helicase MSS116, mitochondrial / Mss116p


Mass: 29127.637 Da / Num. of mol.: 2 / Fragment: Domain 2 (UNP residues 342-596)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MSS116, YDR194C, YD9346.05C / Organelle: mitochondrion / Plasmid: pMAL-c2t / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2 / References: UniProt: P15424, RNA helicase
#2: DNA/RNA hybrid
5'-R(*GP*GP*GP*CP*GP*GP*G)-D(P*CP*CP*CP*GP*CP*CP*C)-3'


Mass: 4395.755 Da / Num. of mol.: 4 / Source method: obtained synthetically

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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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 6% tacsimate, pH 5.0, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2011
RadiationMonochromator: Double-crystal Si(111), liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 3.599→50 Å / Num. obs: 8213 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 13.2
Reflection shellResolution: 3.599→3.66 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.7 / % possible all: 98

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASER2.3.0phasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I5X

3i5x


Resolution: 3.599→42.818 Å / SU ML: 0.36 / σ(F): 1.33 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 828 10.08 %RANDOM
Rwork0.2446 ---
obs0.2482 8213 90 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.054 Å2 / ksol: 0.27 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.8663 Å20 Å20 Å2
2--6.7655 Å2-0 Å2
3---1.1009 Å2
Refinement stepCycle: LAST / Resolution: 3.599→42.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3609 1163 0 0 4772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054975
X-RAY DIFFRACTIONf_angle_d0.9637051
X-RAY DIFFRACTIONf_dihedral_angle_d12.7611802
X-RAY DIFFRACTIONf_chiral_restr0.054875
X-RAY DIFFRACTIONf_plane_restr0.005715
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1757X-RAY DIFFRACTIONPOSITIONAL0.024
12B1757X-RAY DIFFRACTIONPOSITIONAL0.024
21C159X-RAY DIFFRACTIONPOSITIONAL0.018
22D159X-RAY DIFFRACTIONPOSITIONAL0.018
23E159X-RAY DIFFRACTIONPOSITIONAL0.045
24F159X-RAY DIFFRACTIONPOSITIONAL0.054
31C112X-RAY DIFFRACTIONPOSITIONAL0.031
32D112X-RAY DIFFRACTIONPOSITIONAL0.031
33E112X-RAY DIFFRACTIONPOSITIONAL0.046
34F111X-RAY DIFFRACTIONPOSITIONAL0.071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.599-3.82470.3484980.3179882X-RAY DIFFRACTION40
3.8247-4.11980.36391220.28541101X-RAY DIFFRACTION49
4.1198-4.5340.2781300.24421171X-RAY DIFFRACTION53
4.534-5.18910.26681350.22921209X-RAY DIFFRACTION55
5.1891-6.53390.3241380.27671256X-RAY DIFFRACTION56
6.5339-42.82090.23182050.21131766X-RAY DIFFRACTION80

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