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- PDB-5oc5: Crystal structure of human tRNA-dihydrouridine(20) synthase dsRBD... -

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Basic information

Entry
Database: PDB / ID: 5oc5
TitleCrystal structure of human tRNA-dihydrouridine(20) synthase dsRBD K419A-K420A 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 / NADPH binding / antiviral innate immune response / 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 / NADPH binding / antiviral innate immune response / PKR-mediated signaling / FMN binding / flavin adenine dinucleotide binding / double-stranded RNA binding / tRNA binding / endoplasmic reticulum / mitochondrion / 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 ...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: 1.893 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,9606
Polymers13,6121
Non-polymers3475
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-17 kcal/mol
Surface area6270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.170, 36.170, 75.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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: 13612.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUS2, DUS2L / Plasmid: pET11d / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 35% PEG 4K 1 M LiCl 100 mM Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.893→36.17 Å / Num. obs: 7680 / % possible obs: 99.51 % / Redundancy: 9.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.3
Reflection shellResolution: 1.893→1.961 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.29 / Num. unique obs: 710 / CC1/2: 0.468 / % possible all: 96.33

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wft

4wft


Resolution: 1.893→36.17 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 29.08
RfactorNum. reflection% reflection
Rfree0.2262 768 10.01 %
Rwork0.1688 --
obs0.1747 7670 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.893→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 0 20 56 813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015765
X-RAY DIFFRACTIONf_angle_d1.1381029
X-RAY DIFFRACTIONf_dihedral_angle_d18.072474
X-RAY DIFFRACTIONf_chiral_restr0.073119
X-RAY DIFFRACTIONf_plane_restr0.008128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8926-2.03870.37461460.32081342X-RAY DIFFRACTION97
2.0387-2.24390.25771550.19441396X-RAY DIFFRACTION100
2.2439-2.56850.25961510.17041365X-RAY DIFFRACTION100
2.5685-3.23570.22941580.17431397X-RAY DIFFRACTION100
3.2357-36.17660.19261580.14371402X-RAY DIFFRACTION100

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