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- PDB-4tz6: DEAD-box helicase Mss116 bound to ssRNA and UDP-BeF -

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Basic information

Entry
Database: PDB / ID: 4tz6
TitleDEAD-box helicase Mss116 bound to ssRNA and UDP-BeF
Components
  • ATP-dependent RNA helicase MSS116, mitochondrial
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
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 / 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
BERYLLIUM TRIFLUORIDE ION / URIDINE-5'-DIPHOSPHATE / RNA / ATP-dependent RNA helicase MSS116, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.209 Å
AuthorsMallam, A.L. / Sidote, D.J. / Lambowitz, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2014
Title: Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase.
Authors: Mallam, A.L. / Sidote, D.J. / Lambowitz, A.M.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: ATP-dependent RNA helicase MSS116, mitochondrial
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5985
Polymers60,1032
Non-polymers4943
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-30 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.757, 126.506, 55.510
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


Mass: 57843.730 Da / Num. of mol.: 1 / Fragment: UNP residues 88-596
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MSS116, YDR194C, YD9346.05C / Plasmid: pMAL-c2t / Production host: Escherichia coli (E. coli) / References: UniProt: P15424, RNA helicase
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2259.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M DL-malic acid, pH 7.0, 12 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.209→47.211 Å / Num. obs: 10514 / % possible obs: 96.72 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 5.6
Reflection shellResolution: 3.209→3.36 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.5 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1583)refinement
PHASERphasing
HKL-2000data collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I5X

3i5x


Resolution: 3.209→47.211 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 505 4.8 %
Rwork0.2195 --
obs0.2221 10514 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.209→47.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 154 30 0 4002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034085
X-RAY DIFFRACTIONf_angle_d0.7535575
X-RAY DIFFRACTIONf_dihedral_angle_d13.1081504
X-RAY DIFFRACTIONf_chiral_restr0.031667
X-RAY DIFFRACTIONf_plane_restr0.003686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.209-3.53130.37361170.25932193X-RAY DIFFRACTION87
3.5313-4.0420.30311080.23682557X-RAY DIFFRACTION100
4.042-5.09160.21481400.19922572X-RAY DIFFRACTION100
5.0916-47.2160.26581400.21192687X-RAY DIFFRACTION100

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