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- PDB-4wft: Crystal structure of tRNA-dihydrouridine(20) synthase dsRBD domain -

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Basic information

Entry
Database: PDB / ID: 4wft
TitleCrystal structure of tRNA-dihydrouridine(20) synthase dsRBD domain
ComponentstRNA-dihydrouridine(20) synthase [NAD(P)+]-like
KeywordsRNA BINDING PROTEIN / RNA BINDING PROTEIN OXIDOREDUCTASE
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 / double-stranded RNA 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 / double-stranded RNA binding / FMN 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 / SAD / Resolution: 1.7 Å
AuthorsBou-Nader, C. / Pecqueur, L. / Kamah, A. / Bregeon, D. / Golinelli-Pimpaneau, B. / Guimaraes, B.G. / Fontecave, M. / Hamdane, D.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: An extended dsRBD is required for post-transcriptional modification in human tRNAs.
Authors: Bou-Nader, C. / Pecqueur, L. / Bregeon, D. / Kamah, A. / Guerineau, V. / Golinelli-Pimpaneau, B. / Guimaraes, B.G. / Fontecave, M. / Hamdane, D.
History
DepositionSep 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2
Item: _audit_author.name / _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
C: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
A: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
B: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like


Theoretical massNumber of molelcules
Total (without water)41,1863
Polymers41,1863
Non-polymers00
Water6,612367
1
C: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like


Theoretical massNumber of molelcules
Total (without water)13,7291
Polymers13,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like


Theoretical massNumber of molelcules
Total (without water)13,7291
Polymers13,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like


Theoretical massNumber of molelcules
Total (without water)13,7291
Polymers13,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.130, 55.130, 114.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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.: 3 / Fragment: UNP residues 338-450
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) / Variant (production host): STAR Codon Plus
References: UniProt: Q9NX74, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: Protein 20 mg/mL precipitant: HEPES 100 mM pH 6.5, sodium acetate 100 mM, PEG 2000 MME 30%

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 111
SYNCHROTRONSOLEIL PROXIMA 121.7712
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELMar 17, 2014
PSI PILATUS 6M2PIXELSep 23, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.77121
ReflectionResolution: 1.7→39.74 Å / Num. all: 38156 / Num. obs: 38156 / % possible obs: 99.69 % / Redundancy: 4.51 % / Net I/σ(I): 22.06
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.3364 / Mean I/σ(I) obs: 4.16 / % possible all: 97.65

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→39.738 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1802 1876 5 %
Rwork0.163 --
obs0.1639 37509 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→39.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 0 367 2609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072281
X-RAY DIFFRACTIONf_angle_d1.0473076
X-RAY DIFFRACTIONf_dihedral_angle_d14.409888
X-RAY DIFFRACTIONf_chiral_restr0.045347
X-RAY DIFFRACTIONf_plane_restr0.005388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.74610.2411440.21632729X-RAY DIFFRACTION100
1.7461-1.79750.23451430.1872732X-RAY DIFFRACTION100
1.7975-1.85550.22641450.19242739X-RAY DIFFRACTION100
1.8555-1.92190.21111420.1772704X-RAY DIFFRACTION100
1.9219-1.99880.19441450.16552748X-RAY DIFFRACTION100
1.9988-2.08980.19041440.16042741X-RAY DIFFRACTION100
2.0898-2.19990.21861450.16892764X-RAY DIFFRACTION100
2.1999-2.33780.18971440.17112726X-RAY DIFFRACTION100
2.3378-2.51820.21791440.17222748X-RAY DIFFRACTION100
2.5182-2.77160.19781450.17342740X-RAY DIFFRACTION100
2.7716-3.17250.16811430.17282728X-RAY DIFFRACTION100
3.1725-3.99640.15681450.14392754X-RAY DIFFRACTION100
3.9964-39.74860.14631470.1482780X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -16.2405 Å / Origin y: -1.2345 Å / Origin z: 4.3064 Å
111213212223313233
T0.1552 Å20.021 Å2-0.0378 Å2-0.1141 Å20.0165 Å2--0.1296 Å2
L0.1485 °20.1647 °2-0.2319 °2-0.9709 °2-0.0154 °2--0.1226 °2
S-0.0113 Å °-0.0639 Å °0.0137 Å °-0.1013 Å °0.01 Å °-0.0322 Å °-0.011 Å °-0.0524 Å °-0.0017 Å °
Refinement TLS groupSelection details: all

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