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- PDB-4zox: Crystal structure of the Saccharomyces cerevisiae Sqt1 bound to t... -

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Basic information

Entry
Database: PDB / ID: 4zox
TitleCrystal structure of the Saccharomyces cerevisiae Sqt1 bound to the N-terminus of the ribosomal protein L10
Components
  • 60S ribosomal protein L10
  • Ribosome assembly protein SQT1
KeywordsCHAPERONE / ribosomal biogenesis / WD40 - repeat
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / translational termination / ribosomal large subunit biogenesis / unfolded protein binding / ribosomal large subunit assembly ...SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / translational termination / ribosomal large subunit biogenesis / unfolded protein binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / translation / cytosol / cytoplasm
Similarity search - Function
: / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily ...: / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Ribosome assembly protein SQT1 / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPausch, P. / Altegoer, F. / Bange, G.
CitationJournal: Nat Commun / Year: 2015
Title: Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones.
Authors: Pausch, P. / Singh, U. / Ahmed, Y.L. / Pillet, B. / Murat, G. / Altegoer, F. / Stier, G. / Thoms, M. / Hurt, E. / Sinning, I. / Bange, G. / Kressler, D.
History
DepositionMay 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 assembly protein SQT1
B: 60S ribosomal protein L10


Theoretical massNumber of molelcules
Total (without water)44,9032
Polymers44,9032
Non-polymers00
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-3 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.273, 89.252, 53.559
Angle α, β, γ (deg.)90.00, 100.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

21A-845-

HOH

31A-904-

HOH

41A-1029-

HOH

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Components

#1: Protein Ribosome assembly protein SQT1


Mass: 41408.727 Da / Num. of mol.: 1 / Fragment: UNP residues 53-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SQT1, YIR012W, YIB12W / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35184
#2: Protein/peptide 60S ribosomal protein L10 / rpl10 / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 3494.010 Da / Num. of mol.: 1 / Fragment: UNP residues 1-20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPL10, GRC5, QSR1, YLR075W / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41805
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ca-acetate, 0.1 M Nacacodylate pH 6.5, 40% (v/v) PEG600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 1.6→44.63 Å / Num. obs: 44971 / % possible obs: 99.4 % / Redundancy: 4 % / Net I/σ(I): 18.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1685refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZOV

4zov


Resolution: 1.6→44.626 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1806 2267 5.04 %
Rwork0.1461 --
obs0.1479 44971 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→44.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 0 559 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073078
X-RAY DIFFRACTIONf_angle_d1.1274171
X-RAY DIFFRACTIONf_dihedral_angle_d13.4651090
X-RAY DIFFRACTIONf_chiral_restr0.044470
X-RAY DIFFRACTIONf_plane_restr0.005537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63480.19421230.152599X-RAY DIFFRACTION97
1.6348-1.67290.19331510.14322663X-RAY DIFFRACTION100
1.6729-1.71470.18631310.15092673X-RAY DIFFRACTION100
1.7147-1.76110.17651560.14072658X-RAY DIFFRACTION100
1.7611-1.81290.19181460.14092669X-RAY DIFFRACTION100
1.8129-1.87140.17451440.1462645X-RAY DIFFRACTION99
1.8714-1.93830.17831430.14192648X-RAY DIFFRACTION99
1.9383-2.01590.17241440.14292650X-RAY DIFFRACTION100
2.0159-2.10760.20131360.14642674X-RAY DIFFRACTION100
2.1076-2.21870.1851420.14732681X-RAY DIFFRACTION100
2.2187-2.35770.191480.15422662X-RAY DIFFRACTION99
2.3577-2.53980.17641490.15752653X-RAY DIFFRACTION99
2.5398-2.79530.2051270.16422706X-RAY DIFFRACTION100
2.7953-3.19970.18941470.15312691X-RAY DIFFRACTION100
3.1997-4.03090.16341440.13582677X-RAY DIFFRACTION100
4.0309-44.64330.1621360.13522755X-RAY DIFFRACTION100

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