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- PDB-5by8: The structure of Rpf2-Rrs1 explains its role in ribosome biogenesis -

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Basic information

Entry
Database: PDB / ID: 5by8
TitleThe structure of Rpf2-Rrs1 explains its role in ribosome biogenesis
Components
  • Rpf2
  • Rrs1
KeywordsBIOSYNTHETIC PROTEIN / ribosome biogenesis / Brix domain / protein-RNA interaction / 5S RNP / protein complex
Function / homology
Function and homology information


preribosome, large subunit precursor / 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) / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / ribosomal large subunit assembly / single-stranded RNA binding / rRNA binding / nucleolus
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 production factor 2 homolog / Ribosome biogenesis regulatory protein
Similarity search - Component
Biological speciesEmericella nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.515 Å
AuthorsKharde, S. / Calvino, F.R. / Gumiero, A. / Wild, K. / Sinning, I.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: The structure of Rpf2-Rrs1 explains its role in ribosome biogenesis.
Authors: Kharde, S. / Calvino, F.R. / Gumiero, A. / Wild, K. / Sinning, I.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Rpf2
B: Rrs1


Theoretical massNumber of molelcules
Total (without water)35,4532
Polymers35,4532
Non-polymers00
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-38 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.160, 84.140, 194.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21B-279-

HOH

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Components

#1: Protein Rpf2


Mass: 26315.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans FGSC A4 (mold) / Gene: ANIA_10200 / Production host: Escherichia coli (E. coli) / References: UniProt: C8VMF9
#2: Protein Rrs1


Mass: 9137.579 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans FGSC A4 (mold) / Gene: AN3745.2, ANIA_03745 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5B6T5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M KCl and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.515→42.45 Å / Num. all: 61799 / Num. obs: 61799 / % possible obs: 98 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.6
Reflection shellResolution: 1.515→1.569 Å / Redundancy: 2.4 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 0.7 / % possible all: 84.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.515→42.446 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1908 3074 4.97 %
Rwork0.1455 --
obs0.1478 61794 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.515→42.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 0 425 2955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122671
X-RAY DIFFRACTIONf_angle_d1.3243653
X-RAY DIFFRACTIONf_dihedral_angle_d13.1321055
X-RAY DIFFRACTIONf_chiral_restr0.066429
X-RAY DIFFRACTIONf_plane_restr0.007472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5153-1.53890.35091050.34792096X-RAY DIFFRACTION77
1.5389-1.56420.3691650.32032341X-RAY DIFFRACTION89
1.5642-1.59110.4002920.30462578X-RAY DIFFRACTION95
1.5911-1.62010.33441610.27352619X-RAY DIFFRACTION98
1.6201-1.65120.27971530.24922646X-RAY DIFFRACTION99
1.6512-1.68490.2581400.20762726X-RAY DIFFRACTION100
1.6849-1.72160.23481360.17782660X-RAY DIFFRACTION100
1.7216-1.76160.22081390.16412721X-RAY DIFFRACTION100
1.7616-1.80570.22421460.14992707X-RAY DIFFRACTION100
1.8057-1.85450.22011150.14342689X-RAY DIFFRACTION100
1.8545-1.90910.19611770.13892684X-RAY DIFFRACTION100
1.9091-1.97070.22041620.14152672X-RAY DIFFRACTION100
1.9707-2.04110.17771200.13622740X-RAY DIFFRACTION100
2.0411-2.12280.18941350.12992735X-RAY DIFFRACTION100
2.1228-2.21950.18171260.11952733X-RAY DIFFRACTION100
2.2195-2.33650.2041350.11932721X-RAY DIFFRACTION100
2.3365-2.48280.1815930.1282764X-RAY DIFFRACTION100
2.4828-2.67450.17831390.14082726X-RAY DIFFRACTION100
2.6745-2.94360.18681480.13962750X-RAY DIFFRACTION100
2.9436-3.36940.17351420.13822754X-RAY DIFFRACTION100
3.3694-4.24440.1551750.12792769X-RAY DIFFRACTION100
4.2444-42.46280.16271700.12882889X-RAY DIFFRACTION100

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