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- PDB-4tyy: DEAD-box helicase Mss116 bound to ssRNA and CDP-BeF -

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Basic information

Entry
Database: PDB / ID: 4tyy
TitleDEAD-box helicase Mss116 bound to ssRNA and CDP-BeF
Components
  • ATP-dependent RNA helicase MSS116, mitochondrial
  • RNA (5'-R(P*AP*AP*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 / CYTIDINE-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: 2.74 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 / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / 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_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,2555
Polymers60,7622
Non-polymers4933
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-30 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.635, 126.842, 55.303
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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RNA chain / Protein , 2 types, 2 molecules BA

#1: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2917.895 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) / References: UniProt: P15424, RNA helicase

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Non-polymers , 4 types, 31 molecules

#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


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


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2 M sodium malonate, pH 5.0, 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: Dec 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→47.066 Å / Num. obs: 16982 / % possible obs: 98.62 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.9
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.94 / Rsym value: 0.41 / % possible all: 100

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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: 2.74→47.066 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 853 5.02 %
Rwork0.2234 --
obs0.2256 16982 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.74→47.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 198 30 28 4078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034139
X-RAY DIFFRACTIONf_angle_d0.6295659
X-RAY DIFFRACTIONf_dihedral_angle_d12.9041526
X-RAY DIFFRACTIONf_chiral_restr0.029678
X-RAY DIFFRACTIONf_plane_restr0.003689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.91120.46661490.33522455X-RAY DIFFRACTION92
2.9112-3.13590.34881480.29992635X-RAY DIFFRACTION100
3.1359-3.45140.32891360.26952722X-RAY DIFFRACTION100
3.4514-3.95060.27191390.22912704X-RAY DIFFRACTION100
3.9506-4.97650.23611500.18962721X-RAY DIFFRACTION100
4.9765-47.07260.20061310.18872892X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.78130.83240.11261.16-0.09420.13930.3927-0.065-0.66030.3159-0.2116-0.07580.02420.23150.02870.34360.08450.00760.4626-0.08260.6037128.17116.1586-0.9372
20.6069-0.29370.34930.6233-0.21710.32420.0852-0.69270.08790.52470.17850.1361-0.2523-0.04190.25350.77130.00880.15980.6816-0.25240.4267118.113244.716423.0361
30.8494-0.31670.24270.3237-0.2420.11920.0947-0.01110.85960.1876-0.02820.0032-0.19490.1171-0.0010.5055-0.0240.0120.4697-0.06540.5703123.025540.201611.1358
41.53940.7738-0.54170.5069-0.20721.04950.07510.03250.35880.0035-0.1636-0.3106-0.10320.21060.00050.35360.0007-0.09090.38380.01350.4423131.244435.06077.3894
52.1352-0.99670.33260.5537-0.24190.14640.1159-0.5146-0.98920.224-0.03410.5292-0.0524-0.09450.09290.4979-0.04970.17170.63720.23370.4149107.765412.488921.0039
60.2873-0.122-0.28070.18920.49291.51260.0163-0.1461-0.34350.35390.35310.42040.31010.0210.07390.4771-0.0135-0.00050.4480.14840.9813106.296410.48816.4926
70.62520.62720.06910.7046-0.0630.04260.16490.0191-0.09-0.0128-0.00630.4442-0.1053-0.1076-0.00010.459-0.00920.03530.46970.06320.5292111.523717.300712.0898
82.116-1.39320.06842.79860.62440.26870.0524-0.206-1.04950.32840.00461.01840.030.4779-0.27350.677-0.0956-0.07480.77810.17290.6564106.23161.649415.3661
90.2262-0.30450.14730.3466-0.13140.0740.0267-0.0391-0.3286-0.11240.15280.02870.19150.175-0.00010.5161-0.0126-0.04930.59060.09831.12120.8661-1.436710.9755
100.2968-0.1132-0.00730.14490.29140.88690.52450.0507-0.5870.310.51310.73170.52390.08010.03540.54690.1173-0.05480.708-0.02071.4085124.5099-10.96335.3687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 0 through 8 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 205 )
4X-RAY DIFFRACTION4chain 'A' and (resid 206 through 328 )
5X-RAY DIFFRACTION5chain 'A' and (resid 329 through 370 )
6X-RAY DIFFRACTION6chain 'A' and (resid 371 through 397 )
7X-RAY DIFFRACTION7chain 'A' and (resid 398 through 493 )
8X-RAY DIFFRACTION8chain 'A' and (resid 494 through 522 )
9X-RAY DIFFRACTION9chain 'A' and (resid 523 through 563 )
10X-RAY DIFFRACTION10chain 'A' and (resid 564 through 595 )

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