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- PDB-6ei8: Crystal structure of human tRNA-dihydrouridine (20) synthase dsRB... -

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Basic information

Entry
Database: PDB / ID: 6ei8
TitleCrystal structure of human tRNA-dihydrouridine (20) synthase dsRBD F359A mutant
ComponentstRNA-dihydrouridine(20) synthase [NAD(P)+]-like
KeywordsRNA BINDING PROTEIN / double-stranded RNA-binding domain
Function / homology
Function and homology information


tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / antiviral innate immune response / NADPH binding / PKR-mediated signaling / FMN binding ...tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / antiviral innate immune response / NADPH binding / PKR-mediated signaling / FMN binding / double-stranded RNA binding / flavin adenine dinucleotide binding / tRNA binding / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
DUS2, double-stranded RNA binding domain / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain ...DUS2, double-stranded RNA binding domain / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / Aldolase-type TIM barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBou-Nader, C. / Pecqueur, L. / Hamdane, D.
CitationJournal: Biochemistry / Year: 2019
Title: Conformational Stability Adaptation of a Double-Stranded RNA-Binding Domain to Transfer RNA Ligand.
Authors: Bou-Nader, C. / Pecqueur, L. / Barraud, P. / Fontecave, M. / Tisne, C. / Sacquin-Mora, S. / Hamdane, D.
History
DepositionSep 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity / Item: _citation.title / _entity.formula_weight
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 5, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9414
Polymers13,6531
Non-polymers2883
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-28 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.110, 81.110, 56.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein tRNA-dihydrouridine(20) synthase [NAD(P)+]-like / Dihydrouridine synthase 2 / Up-regulated in lung cancer protein 8 / URLC8 / tRNA-dihydrouridine ...Dihydrouridine synthase 2 / Up-regulated in lung cancer protein 8 / URLC8 / tRNA-dihydrouridine synthase 2-like / hDUS2


Mass: 13652.602 Da / Num. of mol.: 1 / Fragment: UNP residues 338-450 / Mutation: F359A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUS2, DUS2L / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NX74, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.9 Å3/Da / Density % sol: 68.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2M ammonium sulfate 50 mM sodium cacodylate 15 mM magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.25→43.81 Å / Num. obs: 10384 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 57.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.2334 / Net I/σ(I): 9.34
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 1020 / CC1/2: 0.746 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wft

4wft


Resolution: 2.25→43.81 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.846 / SU R Cruickshank DPI: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.211 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.183
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1038 10 %RANDOM
Rwork0.259 ---
obs0.262 10383 100 %-
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.9624 Å20 Å20 Å2
2---4.9624 Å20 Å2
3---9.9248 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.25→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms768 0 15 52 835
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01806HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.081094HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d287SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes20HARMONIC2
X-RAY DIFFRACTIONt_gen_planes113HARMONIC5
X-RAY DIFFRACTIONt_it806HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion18.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion104SEMIHARMONIC5
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_contact904SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.52 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2292 289 10 %
Rwork0.2123 2600 -
all0.214 2889 -
obs--99.97 %

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