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- PDB-3sqw: Structure of Mss116p (NTE deletion) bound to ssRNA and AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 3sqw
TitleStructure of Mss116p (NTE deletion) bound to ssRNA and AMP-PNP
Components
  • ATP-dependent RNA helicase MSS116, mitochondrial
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE/RNA / RecA fold / RNA dependent ATPase / RNA helicase / Mitochondrion / HYDROLASE-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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / ATP-dependent RNA helicase MSS116, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.909 Å
AuthorsDel Campo, M. / Lambowitz, A.M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: High-Throughput Genetic Identification of Functionally Important Regions of the Yeast DEAD-Box Protein Mss116p.
Authors: Mohr, G. / Del Campo, M. / Turner, K.G. / Gilman, B. / Wolf, R.Z. / Lambowitz, A.M.
History
DepositionJul 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7824
Polymers69,2512
Non-polymers5312
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-32 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.159, 126.630, 56.247
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: 66234.312 Da / Num. of mol.: 1 / Fragment: UNP Residues 88-664
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: MSS116, YD9346.05C, YDR194C / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: P15424, RNA helicase
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3016.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM ammonium acetate, 20 mM MgCl2, 50 mM HEPES-Na pH 7.0, and 5% polyethylene glycol 8000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2009
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 48576 / Num. obs: 48576 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Rsym value: 0.084 / Net I/σ(I): 30.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.748 / % possible all: 87.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I5X CHAIN A

3i5x


Resolution: 1.909→31.53 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23729 2430 5 %RANDOM
Rwork0.191 ---
obs0.1933 45960 97.3 %-
all-45960 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.325 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2---0.93 Å20 Å2
3---1.81 Å2
Refinement stepCycle: LAST / Resolution: 1.909→31.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 137 32 187 4350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224287
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2922.0295831
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6565521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71524.722180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68315780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6261524
X-RAY DIFFRACTIONr_chiral_restr0.0740.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02809
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.561.52559
X-RAY DIFFRACTIONr_mcbond_other0.131.51023
X-RAY DIFFRACTIONr_mcangle_it1.06724166
X-RAY DIFFRACTIONr_scbond_it1.77131728
X-RAY DIFFRACTIONr_scangle_it2.9244.51658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.909→1.958 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 166 -
Rwork0.322 2766 -
obs--81.38 %
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)
11.62790.55350.06921.89-0.45170.5263-0.0078-0.19220.18230.27440.00390.0548-0.11610.03640.00390.24920.02240.01430.1731-0.01350.416372.86129.97712.019
21.79930.4939-0.09883.0220.21362.459-0.0327-0.2357-0.37190.22820.11810.02540.13630.0789-0.08530.26670.0545-0.01810.1590.10510.545370.2421.34215.582
310.6957-5.27262.27844.8773-2.58896.0120.38060.2908-0.3326-0.6969-0.1918-0.22360.72510.5255-0.18880.28410.10060.04550.07890.0410.655978.91-10.2246.035
46.68532.2961-1.526431.4602-0.06090.8853-0.28750.1001-0.949-1.04110.2794-1.86990.06410.16920.00820.2929-0.00390.06360.2178-0.04520.549979.3911.4584.69
528.1586.6278-2.75166.4785-3.941412.1178-0.68490.722-1.9045-1.46110.667-1.00080.03781.09330.0180.538-0.1890.19560.4116-0.14280.623483.28222.505-3.095
62.7013.61033.21124.8264.29253.8184-0.0641-0.18360.2385-0.103-0.22790.3192-0.0946-0.21410.2920.12480.03070.06360.0599-0.04130.237865.45833.95416.718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 479
2X-RAY DIFFRACTION2A480 - 560
3X-RAY DIFFRACTION3A561 - 595
4X-RAY DIFFRACTION4B2 - 5
5X-RAY DIFFRACTION5B6 - 9
6X-RAY DIFFRACTION6A800

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