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- PDB-4db2: Mss116p DEAD-box helicase domain 2 bound to an RNA duplex -

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Basic information

Entry
Database: PDB / ID: 4db2
TitleMss116p DEAD-box helicase domain 2 bound to an RNA duplex
Components
  • 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'
  • ATP-dependent RNA helicase MSS116, mitochondrial
KeywordsRNA BINDING PROTEIN/RNA / DEAD-box / RNA helicase / hydrolase / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


Group II intron splicing / transcription elongation by mitochondrial RNA polymerase / mitochondrial RNA processing / RNA strand annealing activity / Group I intron splicing / RNA folding / mRNA processing / regulation of translation / RNA helicase activity / RNA helicase ...Group II intron splicing / transcription elongation by mitochondrial RNA polymerase / mitochondrial RNA processing / RNA strand annealing activity / Group I intron splicing / RNA folding / mRNA processing / regulation of translation / 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 / DEAD/DEAH box helicase domain / 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 / DEAD/DEAH box helicase domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / ATP-dependent RNA helicase MSS116, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.157 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
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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: ATP-dependent RNA helicase MSS116, mitochondrial
D: ATP-dependent RNA helicase MSS116, mitochondrial
E: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'
F: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'
G: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'
H: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'
I: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'
J: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)144,21010
Polymers144,21010
Non-polymers00
Water0
1
A: ATP-dependent RNA helicase MSS116, mitochondrial
C: ATP-dependent RNA helicase MSS116, mitochondrial
E: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'
F: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)67,5974
Polymers67,5974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-43 kcal/mol
Surface area25860 Å2
MethodPISA
2
B: ATP-dependent RNA helicase MSS116, mitochondrial
D: ATP-dependent RNA helicase MSS116, mitochondrial
I: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'
J: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)67,5974
Polymers67,5974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-46 kcal/mol
Surface area25440 Å2
MethodPISA
3
G: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'
H: 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)9,0162
Polymers9,0162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-6 kcal/mol
Surface area5260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.534, 88.422, 121.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 29290.809 Da / Num. of mol.: 4 / 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: RNA chain
5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'


Mass: 4507.755 Da / Num. of mol.: 6 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% tacsimate, pH 6.0, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 15, 2011 / Details: VariMax HighFlux
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.15→121.238 Å / Num. all: 30564 / Num. obs: 30146 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.7
Reflection shellResolution: 3.15→3.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.3 / % possible all: 94.8

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Processing

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

3i5x


Resolution: 3.157→42.624 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 1518 5.04 %
Rwork0.2244 --
obs0.2266 30107 99.17 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.845 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.6597 Å2-0 Å20 Å2
2---14.2654 Å2-0 Å2
3---24.9251 Å2
Refinement stepCycle: LAST / Resolution: 3.157→42.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7716 1761 0 0 9477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029812
X-RAY DIFFRACTIONf_angle_d0.63413692
X-RAY DIFFRACTIONf_dihedral_angle_d12.4283852
X-RAY DIFFRACTIONf_chiral_restr0.0421669
X-RAY DIFFRACTIONf_plane_restr0.0021448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.157-3.25870.32721190.3082421X-RAY DIFFRACTION94
3.2587-3.37510.32331570.29272568X-RAY DIFFRACTION100
3.3751-3.51020.3361260.26842570X-RAY DIFFRACTION100
3.5102-3.66990.29041290.25632601X-RAY DIFFRACTION100
3.6699-3.86330.3061380.2552565X-RAY DIFFRACTION100
3.8633-4.10510.28421340.23082588X-RAY DIFFRACTION99
4.1051-4.42180.2631420.19922606X-RAY DIFFRACTION100
4.4218-4.86620.27211330.18192620X-RAY DIFFRACTION100
4.8662-5.5690.30271440.21032620X-RAY DIFFRACTION100
5.569-7.01130.26681460.22342656X-RAY DIFFRACTION100
7.0113-42.6280.19191500.19952774X-RAY DIFFRACTION99

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