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- PDB-6h57: Crystal structure of S. cerevisiae DEAH-box RNA helicase Dhr1, es... -

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Basic information

Entry
Database: PDB / ID: 6h57
TitleCrystal structure of S. cerevisiae DEAH-box RNA helicase Dhr1, essential for small ribosomal subunit biogenesis
ComponentsProbable ATP-dependent RNA helicase DHR1
KeywordsHYDROLASE / protein
Function / homology
Function and homology information


Major pathway of rRNA processing in the nucleolus and cytosol / helicase activity / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / ribosome biogenesis / RNA helicase activity / RNA helicase / nucleolus ...Major pathway of rRNA processing in the nucleolus and cytosol / helicase activity / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / ribosome biogenesis / RNA helicase activity / RNA helicase / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding
Similarity search - Function
: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase ...: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Probable ATP-dependent RNA helicase DHR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRoychowdhury, A. / Graille, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE09-0016-02 France
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: The DEAH-box RNA helicase Dhr1 contains a remarkable carboxyl terminal domain essential for small ribosomal subunit biogenesis.
Authors: Roychowdhury, A. / Joret, C. / Bourgeois, G. / Heurgue-Hamard, V. / Lafontaine, D.L.J. / Graille, M.
History
DepositionJul 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DHR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,20620
Polymers145,1711
Non-polymers1,03519
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-10 kcal/mol
Surface area38980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.314, 115.800, 157.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable ATP-dependent RNA helicase DHR1 / DEAH box RNA helicase DHR1 / Extracellular mutant protein 16


Mass: 145171.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ECM16, DHR1, YMR128W, YM9553.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: UniProt: Q04217, RNA helicase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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

Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2; 0.1 M Tris pH 8.5 and 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.3→48.83 Å / Num. obs: 45887 / % possible obs: 97.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 47.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.067 / Rrim(I) all: 0.131 / Net I/σ(I): 8.6 / Num. measured all: 157599
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.383.30.99545080.4760.6111.17698.6
8.91-48.833.20.0238390.9990.0140.02791.4

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KX2

3kx2


Resolution: 2.3→48.83 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.902 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.288 / SU Rfree Blow DPI: 0.217 / SU Rfree Cruickshank DPI: 0.217
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2174 4.74 %RANDOM
Rwork0.205 ---
obs0.207 45851 96.7 %-
Displacement parametersBiso max: 128.35 Å2 / Biso mean: 45.2 Å2 / Biso min: 20.35 Å2
Baniso -1Baniso -2Baniso -3
1-5.5837 Å20 Å20 Å2
2--4.0767 Å20 Å2
3----9.6603 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.3→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6340 0 61 274 6675
Biso mean--53.25 41.21 -
Num. residues----795
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2348SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes154HARMONIC2
X-RAY DIFFRACTIONt_gen_planes927HARMONIC5
X-RAY DIFFRACTIONt_it6538HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion855SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7516SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6538HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8800HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion20.97
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 149 4.4 %
Rwork0.23 3238 -
all0.232 3387 -
obs--98.81 %
Refinement TLS params.Method: refined / Origin x: -21.0332 Å / Origin y: -12.7859 Å / Origin z: 28.1618 Å
111213212223313233
T-0.0993 Å2-0.0138 Å20.0176 Å2--0.0773 Å2-0.0186 Å2---0.0214 Å2
L0.2632 °2-0.114 °2-0.0059 °2-0.3913 °2-0.0541 °2--0.1666 °2
S0.037 Å °-0.0142 Å °0.0197 Å °-0.0044 Å °-0.0641 Å °-0.0381 Å °0.0088 Å °-0.0007 Å °0.0271 Å °
Refinement TLS groupSelection details: { C|* }

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