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- PDB-5wxl: Crystal structure of the Rrs1 and Rpf2 complex -

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Basic information

Entry
Database: PDB / ID: 5wxl
TitleCrystal structure of the Rrs1 and Rpf2 complex
Components
  • Regulator of ribosome biosynthesis
  • Ribosome biogenesis protein RPF2
KeywordsNUCLEAR PROTEIN / protein complex / components of 90S preribosome
Function / homology
Function and homology information


7S RNA binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / ribosomal large subunit assembly ...7S RNA binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / ribosomal large subunit assembly / 5S rRNA binding / rRNA binding / nucleolus / nucleoplasm
Similarity search - Function
Ribosome biogenesis protein Rpf2 / Ribosomal biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / Brix domain / Brix domain / Brix domain profile. / Brix
Similarity search - Domain/homology
Ribosome biogenesis protein RPF2 / Regulator of ribosome biosynthesis
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsYe, K. / Zheng, S.
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 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 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

Downloads & links

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Assembly

Deposited unit
A: Ribosome biogenesis protein RPF2
B: Regulator of ribosome biosynthesis
C: Ribosome biogenesis protein RPF2
D: Regulator of ribosome biosynthesis


Theoretical massNumber of molelcules
Total (without water)85,8764
Polymers85,8764
Non-polymers00
Water10,809600
1
A: Ribosome biogenesis protein RPF2
B: Regulator of ribosome biosynthesis


Theoretical massNumber of molelcules
Total (without water)42,9382
Polymers42,9382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-24 kcal/mol
Surface area14670 Å2
MethodPISA
2
C: Ribosome biogenesis protein RPF2
D: Regulator of ribosome biosynthesis


Theoretical massNumber of molelcules
Total (without water)42,9382
Polymers42,9382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-24 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.791, 71.791, 268.905
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ribosome biogenesis protein RPF2 / Rpf2


Mass: 31323.627 Da / Num. of mol.: 2 / Fragment: UNP residues 19-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: RPF2, YKR081C, YKR401 / Production host: Escherichia coli (E. coli) / References: UniProt: P36160
#2: Protein Regulator of ribosome biosynthesis / Rrs1


Mass: 11614.231 Da / Num. of mol.: 2 / Fragment: UNP residues 20-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: RRS1, YOR294W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08746
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 47.2 % / Mosaicity: 0.219 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Trimethylamine N-oxide, 0.1 M Tris-HCl, 20% PEG2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.00903 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00903 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 64639 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 22.43 Å2 / Rmerge(I) obs: 0.084 / Χ2: 1.243 / Net I/av σ(I): 26.169 / Net I/σ(I): 10.1 / Num. measured all: 387229
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.9-1.936.10.515199.7
1.93-1.976.10.44199.7
1.97-2.016.10.402199.8
2.01-2.056.10.338199.8
2.05-2.096.10.268199.8
2.09-2.146.10.23199.9
2.14-2.196.10.211199.9
2.19-2.256.10.178199.9
2.25-2.326.10.1521100
2.32-2.396.10.1341100
2.39-2.486.10.1281100
2.48-2.586.10.1191100
2.58-2.6960.121100
2.69-2.8460.111100
2.84-3.015.90.0981100
3.01-3.255.90.0891100
3.25-3.575.90.0681100
3.57-4.085.70.0471100
4.08-5.1360.0411100
5.13-205.60.042198.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
PHENIX(1.11rc1_2513: ???)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.805 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 3269 5.07 %
Rwork0.1793 61261 -
obs0.1808 64530 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.53 Å2 / Biso mean: 26.9881 Å2 / Biso min: 9.85 Å2
Refinement stepCycle: final / Resolution: 1.9→19.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 0 600 5470
Biso mean---33.24 -
Num. residues----605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074964
X-RAY DIFFRACTIONf_angle_d0.8666679
X-RAY DIFFRACTIONf_chiral_restr0.053750
X-RAY DIFFRACTIONf_plane_restr0.005859
X-RAY DIFFRACTIONf_dihedral_angle_d9.553091
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.92840.29571380.219825882726100
1.9284-1.95850.26991320.204226832815100
1.9585-1.99060.24111650.202325892754100
1.9906-2.02490.2131480.199125752723100
2.0249-2.06170.21681370.192526492786100
2.0617-2.10130.23811650.184926092774100
2.1013-2.14410.20941470.180526062753100
2.1441-2.19070.22841290.181226292758100
2.1907-2.24160.22721410.183926562797100
2.2416-2.29750.21911430.182826342777100
2.2975-2.35960.23731590.183726042763100
2.3596-2.42890.23071390.185826372776100
2.4289-2.50710.22811280.189926672795100
2.5071-2.59660.25641350.196426732808100
2.5966-2.70030.25251460.196826522798100
2.7003-2.82280.23781570.192226532810100
2.8228-2.97120.2198960.200127322828100
2.9712-3.15670.23381420.191926552797100
3.1567-3.39930.21231480.184626902838100
3.3993-3.73930.20011330.1727152848100
3.7393-4.27560.18931620.148426972859100
4.2756-5.3690.15011530.14927672920100
5.369-19.80560.17451260.17772901302799

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