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- PDB-8jfx: TruB domain of TruB1 -

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Basic information

Entry
Database: PDB / ID: 8jfx
TitleTruB domain of TruB1
ComponentsPseudouridylate synthase TRUB1
KeywordsRNA BINDING PROTEIN / TruB1
Function / homology
Function and homology information


positive regulation of pre-miRNA processing / tRNA pseudouridine55 synthase / tRNA pseudouridine(55) synthase activity / Isomerases; Intramolecular transferases; Transferring other groups / mRNA pseudouridine synthesis / pseudouridine synthase activity / pre-miRNA binding / tRNA modification / mRNA processing / mitochondrion ...positive regulation of pre-miRNA processing / tRNA pseudouridine55 synthase / tRNA pseudouridine(55) synthase activity / Isomerases; Intramolecular transferases; Transferring other groups / mRNA pseudouridine synthesis / pseudouridine synthase activity / pre-miRNA binding / tRNA modification / mRNA processing / mitochondrion / nucleus / cytosol
Similarity search - Function
tRNA pseudouridine synthase II, TruB / Pseudouridine synthase II, N-terminal / TruB family pseudouridylate synthase (N terminal domain) / Pseudouridine synthase, catalytic domain superfamily
Similarity search - Domain/homology
BROMIDE ION / Pseudouridylate synthase TRUB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXuan, Y.M. / Gong, Q.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071221 China
CitationJournal: To Be Published
Title: Structural basis of pri-let-7 recognition by human pseudouridine synthase TruB1
Authors: Xuan, Y.M. / Gong, Q.G.
History
DepositionMay 19, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pseudouridylate synthase TRUB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7733
Polymers28,6131
Non-polymers1602
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-0 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.315, 53.487, 90.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pseudouridylate synthase TRUB1 / TruB pseudouridine synthase homolog 1 / tRNA pseudouridine 55 synthase TRUB1 / Psi55 synthase TRUB1


Mass: 28613.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRUB1, PUS4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WWH5, Isomerases; Intramolecular transferases; Transferring other groups, tRNA pseudouridine55 synthase
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 2000, 0.15M Potassium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.2→46 Å / Num. obs: 12858 / % possible obs: 99.8 % / Redundancy: 10.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.029 / Rrim(I) all: 0.096 / Χ2: 1.01 / Net I/σ(I): 15.5 / Num. measured all: 139128
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.873 / Num. measured all: 12099 / Num. unique obs: 1083 / CC1/2: 0.802 / Rpim(I) all: 0.273 / Rrim(I) all: 0.916 / Χ2: 0.97 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→26.74 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 614 4.79 %
Rwork0.2052 --
obs0.2071 12824 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→26.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 2 53 1766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031742
X-RAY DIFFRACTIONf_angle_d0.5942364
X-RAY DIFFRACTIONf_dihedral_angle_d5.359240
X-RAY DIFFRACTIONf_chiral_restr0.04281
X-RAY DIFFRACTIONf_plane_restr0.003302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.420.32291440.25953009X-RAY DIFFRACTION100
2.42-2.770.28551420.24743006X-RAY DIFFRACTION100
2.77-3.490.28571540.22893056X-RAY DIFFRACTION100
3.49-26.740.20351740.17653139X-RAY DIFFRACTION99
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)
16.7439-0.05833.78031.5257-0.50273.0374-0.06731.40410.1663-0.36380.0042-0.1949-0.03581.06720.0130.28410.00880.05680.6907-0.02280.349426.4275-13.4663-12.4199
21.9872-1.34070.33566.625-1.07394.58930.35630.4628-0.2291-1.5915-0.32720.58970.34690.0344-0.03540.60740.003-0.21270.4014-0.01560.36220.8221-13.1381-30.1756
35.24264.9985.47448.23363.0557.83040.5997-0.17280.1990.1691-0.36580.16040.5879-0.1693-0.21910.24570.0587-0.00780.3485-0.02440.324616.8768-15.2224-5.8051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 144 )
2X-RAY DIFFRACTION2chain 'A' and (resid 145 through 280 )
3X-RAY DIFFRACTION3chain 'A' and (resid 281 through 306 )

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