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- PDB-5wwn: Crystal structure of Tsr1 -

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Basic information

Entry
Database: PDB / ID: 5wwn
TitleCrystal structure of Tsr1
ComponentsRibosome biogenesis protein TSR1
KeywordsRNA BINDING PROTEIN / ribosome biogenesis protein
Function / homology
Function and homology information


endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / preribosome, small subunit precursor / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / ribonucleoprotein complex binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GTPase activity / GTP binding / nucleolus ...endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / preribosome, small subunit precursor / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / ribonucleoprotein complex binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GTPase activity / GTP binding / nucleolus / nucleus / cytoplasm
Similarity search - Function
Tsr1, G-like domain / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663)
Similarity search - Domain/homology
Ribosome biogenesis protein TSR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.805 Å
AuthorsYe, K. / Wang, B.
CitationJournal: Elife / Year: 2017
Title: Molecular architecture of the 90S small subunit pre-ribosome.
Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye /
Abstract: Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the ...Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.
History
DepositionJan 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ribosome biogenesis protein TSR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,87711
Polymers81,9161
Non-polymers96110
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.374, 116.344, 119.463
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosome biogenesis protein TSR1 / 20S rRNA accumulation protein 1


Mass: 81916.039 Da / Num. of mol.: 1 / Fragment: UNP residues 80-788
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TSR1, YDL060W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q07381
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

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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: 2.77 Å3/Da / Density % sol: 55.64 % / Mosaicity: 1.576 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium chloride, 0.08M BIS-TRIS pH 5.5, 0.02M BIS-TRIS pH 6.5, 1.6M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 22912 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 54.59 Å2 / Rmerge(I) obs: 0.16 / Net I/av σ(I): 15.576 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)CC1/2Diffraction-ID% possible allRmerge(I) obs
2.8-2.857.20.3331100
2.85-2.97.20.4271100
2.9-2.967.20.4731100
2.96-3.027.20.5941100
3.02-3.087.20.7241100
3.08-3.157.20.81311000.794
3.15-3.237.20.83611000.649
3.23-3.327.20.92199.90.562
3.32-3.427.20.92911000.489
3.42-3.537.20.95711000.37
3.53-3.657.20.96811000.267
3.65-3.87.10.97511000.211
3.8-3.9770.98311000.197
3.97-4.1870.98911000.167
4.18-4.446.80.99311000.121
4.44-4.796.80.995199.90.1
4.79-5.276.80.99511000.086
5.27-6.036.70.99611000.085
6.03-7.5970.99711000.071
7.59-506.30.997198.80.049

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.805→43.458 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.92
RfactorNum. reflection% reflection
Rfree0.2742 1128 4.94 %
Rwork0.2144 --
obs0.2173 22852 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 210.27 Å2 / Biso mean: 48.9496 Å2 / Biso min: 22.48 Å2
Refinement stepCycle: final / Resolution: 2.805→43.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4347 0 50 0 4397
Biso mean--94.27 --
Num. residues----531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014486
X-RAY DIFFRACTIONf_angle_d1.2846059
X-RAY DIFFRACTIONf_chiral_restr0.052651
X-RAY DIFFRACTIONf_plane_restr0.006775
X-RAY DIFFRACTIONf_dihedral_angle_d19.5371679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8054-2.93310.34621700.27862536270696
2.9331-3.08770.33871300.257227142844100
3.0877-3.28110.30761250.23926922817100
3.2811-3.53430.33331540.233326852839100
3.5343-3.88980.27281330.205627252858100
3.8898-4.45220.25491420.197127162858100
4.4522-5.60740.23741200.18627902910100
5.6074-43.46310.23871540.21272866302099

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