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- PDB-4tyw: DEAD-box helicase Mss116 bound to ssRNA and ADP-BeF -

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Basic information

Entry
Database: PDB / ID: 4tyw
TitleDEAD-box helicase Mss116 bound to ssRNA and ADP-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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / RNA / ATP-dependent RNA helicase MSS116, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å
AuthorsMallam, A.L. / Sidote, D.J. / Lambowitz, A.M.
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 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
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_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)60,5876
Polymers60,0452
Non-polymers5424
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-39 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.829, 126.260, 55.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

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


Mass: 57785.699 Da / Num. of mol.: 1 / Fragment: UNP residues 88-595
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) / 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)

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Non-polymers , 4 types, 119 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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


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


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 2 % tacsimate pH 7.0, 20 % 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: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.197→47.243 Å / Num. obs: 32642 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.54 / Rsym value: 0.444 / % possible all: 97.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I5X

3i5x


Resolution: 2.197→47.243 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 1658 5.08 %
Rwork0.2161 --
obs0.218 32642 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.197→47.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 154 33 115 4249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034219
X-RAY DIFFRACTIONf_angle_d0.6965737
X-RAY DIFFRACTIONf_dihedral_angle_d11.8851600
X-RAY DIFFRACTIONf_chiral_restr0.028676
X-RAY DIFFRACTIONf_plane_restr0.003701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.197-2.26170.34231350.33662395X-RAY DIFFRACTION94
2.2617-2.33470.31571470.29462496X-RAY DIFFRACTION97
2.3347-2.41810.29061140.27292538X-RAY DIFFRACTION97
2.4181-2.51490.33481500.25272522X-RAY DIFFRACTION99
2.5149-2.62940.33851440.24822572X-RAY DIFFRACTION100
2.6294-2.7680.28341580.23592556X-RAY DIFFRACTION100
2.768-2.94140.30971240.23362614X-RAY DIFFRACTION100
2.9414-3.16850.31051180.24022596X-RAY DIFFRACTION100
3.1685-3.48720.26811610.22982598X-RAY DIFFRACTION100
3.4872-3.99160.23741380.20572632X-RAY DIFFRACTION100
3.9916-5.02810.21821110.17212688X-RAY DIFFRACTION100
5.0281-47.25380.18351580.18352777X-RAY DIFFRACTION100

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