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- PDB-4nz7: Steroid receptor RNA Activator (SRA) modification by the human Ps... -

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Basic information

Entry
Database: PDB / ID: 4nz7
TitleSteroid receptor RNA Activator (SRA) modification by the human Pseudouridine Synthase 1 (hPus1p): RNA binding, activity, and atomic model
ComponentstRNA pseudouridine synthase A, mitochondrial
KeywordsISOMERASE / Steroid receptors RNA Activator / pseudouridylation / nuclus / mitochondrial
Function / homology
Function and homology information


mitochondrial tRNA pseudouridine synthesis / steroid receptor RNA activator RNA binding / tRNA pseudouridine38-40 synthase / tRNA modification in the mitochondrion / Isomerases; Intramolecular transferases; Transferring other groups / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification in the nucleus and cytosol ...mitochondrial tRNA pseudouridine synthesis / steroid receptor RNA activator RNA binding / tRNA pseudouridine38-40 synthase / tRNA modification in the mitochondrion / Isomerases; Intramolecular transferases; Transferring other groups / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification in the nucleus and cytosol / RNA splicing / mRNA processing / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Pseudouridine synthase PUS1/ PUS2-like / Pseudouridine synthase I, catalytic domain, C-terminal subdomain / Pseudouridine synthase I, catalytic domain, N-terminal subdomain / Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, catalytic domain superfamily / Alpha-Beta Plaits ...Pseudouridine synthase PUS1/ PUS2-like / Pseudouridine synthase I, catalytic domain, C-terminal subdomain / Pseudouridine synthase I, catalytic domain, N-terminal subdomain / Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, catalytic domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Pseudouridylate synthase 1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHuet, T. / Thore, S.
CitationJournal: Plos One / Year: 2014
Title: Steroid Receptor RNA Activator (SRA) Modification by the Human Pseudouridine Synthase 1 (hPus1p): RNA Binding, Activity, and Atomic Model
Authors: Huet, T. / Miannay, F.-A. / Patton, J.R. / Thore, S.
History
DepositionDec 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA pseudouridine synthase A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0153
Polymers35,6271
Non-polymers3882
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.446, 69.044, 116.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein tRNA pseudouridine synthase A, mitochondrial / tRNA pseudouridine(38-40) synthase / tRNA pseudouridylate synthase I / tRNA-uridine isomerase I


Mass: 35626.867 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 83-394 / Mutation: D146A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUS1, PP8985 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 STAR
References: UniProt: Q9Y606, tRNA pseudouridine38-40 synthase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 17% PEG 8000, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2012
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 9304 / Num. obs: 9281 / % possible obs: 99.8 % / Observed criterion σ(F): 3.43 / Biso Wilson estimate: 31.87 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.7-2.771100
2.77-2.85199.8
2.85-2.93199.8
2.93-3.02199.7
3.02-3.12199.8
3.12-3.231100
3.23-3.351100
3.35-3.491100
3.49-3.64199.6
3.64-3.821100
3.82-4.03199.8
4.03-4.27199.8
4.27-4.561100
4.56-4.93199.8
4.93-5.4199.7
5.4-6.041100
6.04-6.97199.1
6.97-8.54198.9
8.54-12.08199.5
12.08-50196.3

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.879 Å / FOM work R set: 0.8227 / SU ML: 0.33 / σ(F): 1.36 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 922 9.99 %
Rwork0.1833 --
obs0.1889 9231 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.98 Å2 / Biso mean: 17.05 Å2 / Biso min: 3.19 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 25 108 2564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052494
X-RAY DIFFRACTIONf_angle_d0.8633355
X-RAY DIFFRACTIONf_dihedral_angle_d14.105946
X-RAY DIFFRACTIONf_chiral_restr0.065360
X-RAY DIFFRACTIONf_plane_restr0.003428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7003-2.84220.35491310.244311771308100
2.8422-3.01970.29641280.22211581286100
3.0197-3.2520.30921280.200911551283100
3.252-3.57750.26911310.175911801311100
3.5775-4.09130.21051310.162411731304100
4.0913-5.13980.17021320.148611961328100
5.1398-19.87910.21491410.19291270141199

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