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- PDB-5oc6: Crystal structure of human tRNA-dihydrouridine(20) synthase dsRBD... -

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Basic information

Entry
Database: PDB / ID: 5oc6
TitleCrystal structure of human tRNA-dihydrouridine(20) synthase dsRBD in complex with a 22 nucleotide dsRNA
Components
  • RNA
  • tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
KeywordsRNA BINDING PROTEIN / double-stranded RNA-binding domain protein-RNA complex dsRNA
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
RNA / RNA (> 10) / tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBou-nader, C. / Pecqueur, L. / Hamdane, D.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2.
Authors: Bou-Nader, C. / Barraud, P. / Pecqueur, L. / Perez, J. / Velours, C. / Shepard, W. / Fontecave, M. / Tisne, C. / Hamdane, D.
History
DepositionJun 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
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 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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
B: RNA
C: RNA


Theoretical massNumber of molelcules
Total (without water)20,6933
Polymers20,6933
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-18 kcal/mol
Surface area8850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.440, 115.560, 66.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 13728.697 Da / Num. of mol.: 1 / Fragment: UNP residues 338-450
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: RNA chain RNA /


Mass: 3482.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 15% v/v isopropanol 20 mM MgCl2 50 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.2→43.65 Å / Num. obs: 3855 / % possible obs: 97.52 % / Redundancy: 5.8 % / Biso Wilson estimate: 100.05 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.3064 / Net I/σ(I): 5.11
Reflection shellResolution: 3.2→3.314 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 358 / CC1/2: 0.302 / % possible all: 93.44

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Processing

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

4wft


Resolution: 3.2→43.65 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.438
RfactorNum. reflection% reflectionSelection details
Rfree0.242 380 9.86 %RANDOM
Rwork0.226 ---
obs0.228 3855 97.7 %-
Displacement parametersBiso mean: 99.32 Å2
Baniso -1Baniso -2Baniso -3
1-11.5331 Å20 Å20 Å2
2---8.5683 Å20 Å2
3----2.9649 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: 1 / Resolution: 3.2→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms718 468 0 0 1186
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081251HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.851794HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d360SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes16HARMONIC2
X-RAY DIFFRACTIONt_gen_planes125HARMONIC5
X-RAY DIFFRACTIONt_it1251HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion21.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion183SEMIHARMONIC5
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_contact1416SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.58 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.266 100 9.62 %
Rwork0.2417 940 -
all0.2438 1040 -
obs--95.5 %
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)
16.69912.6646-1.27428.3154-2.47125.63300.4908-0.15770.11060.5442-0.30810.2577-0.5442-0.5442-0.01810.0449-0.10950.07030.0555-0.2308-12.7472-11.00385.8448
200.5523-2.91040.18940.30850.8125-0.1997-0.1434-0.46710.54420.21-0.39040.54420.2563-0.01030.0133-0.0442-0.1520.17980.07090.0654-13.9277-27.719316.0777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* },{ C|* }

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