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- PDB-4gmn: Structural basis of Rpl5 recognition by Syo1 -

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Basic information

Entry
Database: PDB / ID: 4gmn
TitleStructural basis of Rpl5 recognition by Syo1
Components
  • 60S ribosomal protein l5-like protein
  • Putative uncharacterized protein
KeywordsRNA BINDING PROTEIN / ARM / HEAT / solenoid / linear motif / nuclear transport / chaperone / ribosome assembly / Rpl11 / Kap104
Function / homology
Function and homology information


ribosomal large subunit biogenesis / protein import into nucleus / unfolded protein binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
: / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Symportin 1 / Large ribosomal subunit protein uL18
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsBange, G. / Sinning, I.
CitationJournal: Science / Year: 2012
Title: Synchronizing nuclear import of ribosomal proteins with ribosome assembly.
Authors: Kressler, D. / Bange, G. / Ogawa, Y. / Stjepanovic, G. / Bradatsch, B. / Pratte, D. / Amlacher, S. / Strauss, D. / Yoneda, Y. / Katahira, J. / Sinning, I. / Hurt, E.
History
DepositionAug 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 60S ribosomal protein l5-like protein
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)80,7822
Polymers80,7822
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-7 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.620, 104.230, 182.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide 60S ribosomal protein l5-like protein


Mass: 6073.017 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063640, Rpl5 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta 2 / References: UniProt: G0SEG2
#2: Protein Putative uncharacterized protein


Mass: 74709.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0033460, Syo1 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta 2 / References: UniProt: G0S5S6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M succinic acid pH 7.0, 20% (v/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9768 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2010
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 2.95→63.27 Å / Num. obs: 16385 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.2
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2358 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→45.239 Å / SU ML: 0.37 / σ(F): 0.01 / Phase error: 25.64 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 1606 10.05 %random
Rwork0.203 ---
obs0.2088 15983 97.76 %-
all-0 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.259 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4542 Å20 Å2-0 Å2
2--15.9509 Å20 Å2
3----12.4967 Å2
Refinement stepCycle: LAST / Resolution: 2.95→45.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4451 0 0 0 4451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094531
X-RAY DIFFRACTIONf_angle_d1.2596158
X-RAY DIFFRACTIONf_dihedral_angle_d17.521662
X-RAY DIFFRACTIONf_chiral_restr0.082737
X-RAY DIFFRACTIONf_plane_restr0.005784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.05540.34931490.27021335X-RAY DIFFRACTION93
3.0554-3.17770.31951540.25921370X-RAY DIFFRACTION95
3.1777-3.32230.31061570.23711397X-RAY DIFFRACTION97
3.3223-3.49740.28921580.23461423X-RAY DIFFRACTION98
3.4974-3.71650.28661610.20781436X-RAY DIFFRACTION99
3.7165-4.00330.25181610.19461444X-RAY DIFFRACTION99
4.0033-4.40580.21231650.16931478X-RAY DIFFRACTION99
4.4058-5.04260.19041630.16781469X-RAY DIFFRACTION99
5.0426-6.35040.31531640.23511471X-RAY DIFFRACTION99
6.3504-45.24450.22941740.17481554X-RAY DIFFRACTION99

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