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- PDB-5a53: Crystal Structure of the Rpf2-Rrs1 complex -

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Basic information

Entry
Database: PDB / ID: 5a53
TitleCrystal Structure of the Rpf2-Rrs1 complex
Components
  • (REGULATOR OF RIBOSOME BIOSYNTHESIS) x 2
  • RIBOSOME BIOGENESIS PROTEIN RPF2
KeywordsTRANSCRIPTION / 5S RNP / RIBOSOME ASSEMBLY / RRS1 / RPF2 / BRIX DOMAIN
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) / nuclear periphery / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 5S rRNA binding ...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) / nuclear periphery / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 5S rRNA binding / ribosomal large subunit assembly / 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 (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.401 Å
AuthorsMadru, C. / Lebaron, S. / Blaud, M. / Delbos, L. / Rety, S. / Leulliot, N.
CitationJournal: Genes Dev. / Year: 2015
Title: Chaperoning 5S RNA Assembly.
Authors: Madru, C. / Lebaron, S. / Blaud, M. / Delbos, L. / Pipoli, J. / Pasmant, E. / Rety, S. / Leulliot, N.
History
DepositionJun 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: REGULATOR OF RIBOSOME BIOSYNTHESIS
B: REGULATOR OF RIBOSOME BIOSYNTHESIS
C: RIBOSOME BIOGENESIS PROTEIN RPF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6977
Polymers36,3133
Non-polymers3844
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-67.6 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.280, 72.280, 175.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-2027-

HOH

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Components

#1: Protein REGULATOR OF RIBOSOME BIOSYNTHESIS


Mass: 7273.322 Da / Num. of mol.: 1 / Fragment: RESIDUES 9-73
Source method: isolated from a genetically manipulated source
Details: TRYPSINOLYZED SAMPLE
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q08746
#2: Protein/peptide REGULATOR OF RIBOSOME BIOSYNTHESIS


Mass: 2463.886 Da / Num. of mol.: 1 / Fragment: RESIDUES 85-106
Source method: isolated from a genetically manipulated source
Details: TRYPSINOLYZED SAMPLE
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q08746
#3: Protein RIBOSOME BIOGENESIS PROTEIN RPF2


Mass: 26575.982 Da / Num. of mol.: 1 / Fragment: BRIX DOMAIN, RESIDUES 23-252
Source method: isolated from a genetically manipulated source
Details: TRYPSINOLYSED SAMPLE
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: P36160
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEOLYZED SAMPLE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 50.8 % / Description: NONE
Crystal growpH: 8
Details: CRYSTALS WERE OBTAINED IN 0.2M LISO4, 30 % (W/V) POLYETHYLENE GLYCOL 4000 AND 0.1 M TRIS-HCL PH 8.5, WITH A COMPLEX SOLUTION AT 15 MG/ML CONTAINING TRYPSIN. CRYSTALS WERE CRYOPROTECTED USING ...Details: CRYSTALS WERE OBTAINED IN 0.2M LISO4, 30 % (W/V) POLYETHYLENE GLYCOL 4000 AND 0.1 M TRIS-HCL PH 8.5, WITH A COMPLEX SOLUTION AT 15 MG/ML CONTAINING TRYPSIN. CRYSTALS WERE CRYOPROTECTED USING SUCCESSIVE SOAKING STEPS IN INCREASING CONCENTRATIONS OF ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.0716
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0716 Å / Relative weight: 1
ReflectionResolution: 2.4→45.51 Å / Num. obs: 18921 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 11.5 % / Biso Wilson estimate: 53.99 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.82
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.92 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.401→45.505 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 942 5 %
Rwork0.1961 --
obs0.1977 18920 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.401→45.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 20 93 2623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022576
X-RAY DIFFRACTIONf_angle_d0.6513476
X-RAY DIFFRACTIONf_dihedral_angle_d12.526996
X-RAY DIFFRACTIONf_chiral_restr0.024394
X-RAY DIFFRACTIONf_plane_restr0.004442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4012-2.52780.31161250.29332465X-RAY DIFFRACTION98
2.5278-2.68620.29451330.25632532X-RAY DIFFRACTION100
2.6862-2.89350.29371320.23492511X-RAY DIFFRACTION100
2.8935-3.18470.26231340.22232538X-RAY DIFFRACTION100
3.1847-3.64530.2631360.21142575X-RAY DIFFRACTION100
3.6453-4.5920.1841360.16952597X-RAY DIFFRACTION100
4.592-45.51360.19331460.17072760X-RAY DIFFRACTION100

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