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- PDB-5c9s: Crystal Structure of the C-terminal domain of Rrp5 -

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Basic information

Entry
Database: PDB / ID: 5c9s
TitleCrystal Structure of the C-terminal domain of Rrp5
ComponentsrRNA biogenesis protein RRP5
KeywordsGENE REGULATION / Ribosome biogenesis / Assembly Factor / TPR
Function / homology
Function and homology information


box H/ACA snoRNA binding / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / 90S preribosome assembly / poly(U) RNA binding / U3 snoRNA binding / snoRNA binding ...box H/ACA snoRNA binding / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / 90S preribosome assembly / poly(U) RNA binding / U3 snoRNA binding / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / 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 SSU-rRNA / small-subunit processome / rRNA processing / mRNA binding / nucleolus / RNA binding / nucleoplasm
Similarity search - Function
: / : / rRNA biogenesis protein Rrp5 / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
rRNA biogenesis protein RRP5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKhoshnevis, S. / Karbstein, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM086451 United States
CitationJournal: Plos Biol. / Year: 2016
Title: Crystal Structure of the C-terminal domain of Rrp5
Authors: Khoshnevis, S. / Karbstein, K.
History
DepositionJun 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 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
B: rRNA biogenesis protein RRP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0762
Polymers64,9841
Non-polymers921
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.140, 114.140, 67.840
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 rRNA biogenesis protein RRP5 / Ribosomal RNA-processing protein 5 / U3 small nucleolar RNA-associated protein RRP5 / U3 snoRNA- ...Ribosomal RNA-processing protein 5 / U3 small nucleolar RNA-associated protein RRP5 / U3 snoRNA-associated protein RRP5


Mass: 64983.922 Da / Num. of mol.: 1 / Fragment: unp residues 1163-1729
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRP5, FMI1, YMR229C, YM9959.11C / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q05022
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.96 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammuniom tartrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9753 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 2.7→57.07 Å / Num. obs: 14309 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 33.94 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.061 / Rrim(I) all: 0.195 / Net I/σ(I): 7.5 / Num. measured all: 141367 / Scaling rejects: 236
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.839.50.681805318930.8480.2310.7193100
8.96-57.079.60.07142224390.9960.0230.07513.799.6

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACT3.14data extraction
Aimlessdata scaling
PHENIXphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→43.672 Å / FOM work R set: 0.8006 / SU ML: 1.04 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 718 5.03 %
Rwork0.2211 13562 -
obs0.2242 14280 99.85 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.686 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 109.94 Å2 / Biso mean: 41.06 Å2 / Biso min: 12.19 Å2
Baniso -1Baniso -2Baniso -3
1--5.3471 Å20 Å20 Å2
2---5.3471 Å20 Å2
3---10.6943 Å2
Refinement stepCycle: final / Resolution: 2.7→43.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 6 53 2317
Biso mean--46.49 27.49 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082307
X-RAY DIFFRACTIONf_angle_d1.0083102
X-RAY DIFFRACTIONf_chiral_restr0.077335
X-RAY DIFFRACTIONf_plane_restr0.004395
X-RAY DIFFRACTIONf_dihedral_angle_d18.005864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7002-2.90870.39321450.289826802825
2.9087-3.20130.31731420.247926652807
3.2013-3.66430.29281560.227226872843
3.6643-4.61590.25351370.190727222859
4.6159-43.67780.23871380.206228082946

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