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- PDB-3sqx: Structure of Mss116p (NTE and C-tail double deletion) bound to ss... -

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Basic information

Entry
Database: PDB / ID: 3sqx
TitleStructure of Mss116p (NTE and C-tail double deletion) bound to ssRNA and AMP-PNP
Components
  • ATP-dependent RNA helicase MSS116, mitochondrial
  • RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE/RNA / RecA fold / RNA dependent ATPase / RNA helicase / DEAD-box protein / 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 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
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: 2.112 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _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 / _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(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6984
Polymers61,1682
Non-polymers5312
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.943, 127.043, 55.883
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: 58151.039 Da / Num. of mol.: 1 / Fragment: UNP Residues 88-597
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(*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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M ammonium tartrate dibasic, pH 7.0, 10% PEG3350, 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: 2.1→30 Å / Num. all: 34638 / Num. obs: 34638 / % possible obs: 95.3 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 6.6 % / Rsym value: 0.094 / Net I/σ(I): 17.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.688 / % possible all: 83.8

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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: 2.112→27.61 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26012 1718 5 %RANDOM
Rwork0.21467 ---
obs0.21696 32796 92.99 %-
all-32796 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2---0.37 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.112→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3985 125 32 103 4245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224224
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2532.0265737
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24524.855173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10515765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7051521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02791
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_it0.4681.52541
X-RAY DIFFRACTIONr_mcbond_other0.1031.51017
X-RAY DIFFRACTIONr_mcangle_it0.86824128
X-RAY DIFFRACTIONr_scbond_it1.42631683
X-RAY DIFFRACTIONr_scangle_it2.3114.51608
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.112→2.167 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 90 -
Rwork0.314 1610 -
obs--62.99 %
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)
115.6651-1.4917-0.19067.8403-5.33410.91620.7125-1.87982.26281.7089-0.06970.9594-1.4537-0.3287-0.64280.8368-0.06490.33640.3127-0.43720.891671.45245.97922.795
22.72041.15590.02682.2302-0.59050.5350.1074-0.2490.17610.2974-0.07180.0627-0.09330.0338-0.03570.30770.00370.03030.07360.00230.392774.05128.25510.907
33.10210.96070.12183.81170.54361.7260.1122-0.3869-0.75460.3119-0.0507-0.15720.23320.0222-0.06150.30330.0172-0.03330.06760.18030.661270.3960.40614.748
48.928-8.81927.095615.4617-0.076312.76350.53991.79940.0469-0.28030.8641-1.35430.75964.1651-1.4040.2980.2550.2341.5087-0.16071.861283.144-9.7515.57
56.757314.26712.921941.25350.41264.27460.09130.3957-0.7836-0.46-0.2023-2.27640.33960.70420.1110.31980.11880.11550.23690.08460.781779.7312.6255.788
613.18989.8064-2.21828.3752-4.974616.3359-0.46941.0334-1.1105-0.60880.3554-0.68780.62011.05570.1140.37720.07670.07920.2399-0.11490.514883.96722.417-3.203
71.5251-0.60261.23148.97855.85755.60090.059-0.2976-0.06050.1521-0.37790.53660.1739-0.58840.31890.1985-0.0240.13830.1489-0.05980.305566.49233.99616.875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 126
2X-RAY DIFFRACTION2A127 - 479
3X-RAY DIFFRACTION3A480 - 567
4X-RAY DIFFRACTION4A568 - 595
5X-RAY DIFFRACTION5B2 - 5
6X-RAY DIFFRACTION6B6 - 9
7X-RAY DIFFRACTION7A800

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