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- PDB-4tyn: DEAD-box helicase Mss116 bound to ssDNA and ADP-BeF -

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Basic information

Entry
Database: PDB / ID: 4tyn
TitleDEAD-box helicase Mss116 bound to ssDNA and ADP-BeF
Components
  • ATP-dependent RNA helicase MSS116, mitochondrial
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsHYDROLASE/DNA / DEAD-box / RNA helicase / hydrolase / RNA BINDING PROTEIN-DNA complex / HYDROLASE-DNA 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 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA processing / regulation of translation / RNA helicase activity ...Group II intron splicing / transcription elongation by mitochondrial RNA polymerase / mitochondrial RNA processing / RNA strand annealing activity / Group I intron splicing / RNA folding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA processing / regulation of translation / RNA helicase activity / RNA helicase / mitochondrial matrix / mRNA binding / nucleolus / 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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / ATP-dependent RNA helicase MSS116, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.959 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 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 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:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,5095
Polymers59,9912
Non-polymers5183
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-14 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.389, 126.189, 55.231
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: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2147.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#2: 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 (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MSS116, YDR194C, YD9346.05C / Plasmid: pMAL-c2t / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2 / References: UniProt: P15424, RNA helicase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium acetate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.959→44.15 Å / Num. obs: 13129 / % possible obs: 94.64 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 8.55
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.46 / Rsym value: 0.491 / % possible all: 88

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1583) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I5X

3i5x


Resolution: 2.959→44.15 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 659 5.03 %Random selection
Rwork0.1962 ---
obs0.1986 13111 95.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.959→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 147 32 0 4089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034181
X-RAY DIFFRACTIONf_angle_d0.7515699
X-RAY DIFFRACTIONf_dihedral_angle_d15.2181548
X-RAY DIFFRACTIONf_chiral_restr0.03673
X-RAY DIFFRACTIONf_plane_restr0.003703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9594-3.18780.34051220.24762105X-RAY DIFFRACTION83
3.1878-3.50850.27591170.22812506X-RAY DIFFRACTION97
3.5085-4.01590.23571400.20562556X-RAY DIFFRACTION99
4.0159-5.05840.21281420.16642600X-RAY DIFFRACTION99
5.0584-44.15530.23271380.18432685X-RAY DIFFRACTION98

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