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- PDB-4bsz: Crystal Structure of the Yeast Ribosomal Protein Rps3 in Complex ... -

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Basic information

Entry
Database: PDB / ID: 4bsz
TitleCrystal Structure of the Yeast Ribosomal Protein Rps3 in Complex with its Chaperone Yar1
Components
  • 40S RIBOSOMAL PROTEIN S3
  • ANKYRIN REPEAT-CONTAINING PROTEIN YAR1
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


MBF transcription complex / SBF transcription complex / response to osmotic stress / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit ...MBF transcription complex / SBF transcription complex / response to osmotic stress / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / 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 / 90S preribosome / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / maintenance of translational fidelity / unfolded protein binding / regulation of protein localization / ribosomal small subunit biogenesis / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / cytosolic small ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / positive regulation of transcription by RNA polymerase II / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
K homology (KH) domain / Ankyrin repeat-containing domain / GMP Synthetase; Chain A, domain 3 / Ribosomal protein S3, eukaryotic/archaeal / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...K homology (KH) domain / Ankyrin repeat-containing domain / GMP Synthetase; Chain A, domain 3 / Ribosomal protein S3, eukaryotic/archaeal / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Alpha Horseshoe / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS3 / Ankyrin repeat-containing protein YAR1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.842 Å
AuthorsHolzer, S. / Ban, N. / Klinge, S.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystal Structure of the Yeast Ribosomal Protein Rps3 in Complex with its Chaperone Yar1
Authors: Holzer, S. / Ban, N. / Klinge, S.
History
DepositionJun 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Structure summary
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Nov 13, 2013Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 40S RIBOSOMAL PROTEIN S3
B: ANKYRIN REPEAT-CONTAINING PROTEIN YAR1


Theoretical massNumber of molelcules
Total (without water)49,5662
Polymers49,5662
Non-polymers00
Water00
1
A: 40S RIBOSOMAL PROTEIN S3
B: ANKYRIN REPEAT-CONTAINING PROTEIN YAR1

A: 40S RIBOSOMAL PROTEIN S3
B: ANKYRIN REPEAT-CONTAINING PROTEIN YAR1

A: 40S RIBOSOMAL PROTEIN S3
B: ANKYRIN REPEAT-CONTAINING PROTEIN YAR1

A: 40S RIBOSOMAL PROTEIN S3
B: ANKYRIN REPEAT-CONTAINING PROTEIN YAR1


Theoretical massNumber of molelcules
Total (without water)198,2648
Polymers198,2648
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area27970 Å2
ΔGint-116.8 kcal/mol
Surface area59890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.830, 104.830, 95.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein 40S RIBOSOMAL PROTEIN S3 / RP13 / YS3


Mass: 26957.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303 / Plasmid: PRSF-DUET1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P05750
#2: Protein ANKYRIN REPEAT-CONTAINING PROTEIN YAR1


Mass: 22608.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303 / Plasmid: PRSF-DUET1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P46683
Sequence detailsTHE CRYSTALLISED CONSTRUCT CONTAINS AN N-TERMINAL ADDITION OF THE RESIDUE SEQUENCE MADP AS A RESULT ...THE CRYSTALLISED CONSTRUCT CONTAINS AN N-TERMINAL ADDITION OF THE RESIDUE SEQUENCE MADP AS A RESULT OF CLONING THE CRYSTALLISED CONSTRUCT CONTAINS AN N-TERMINAL ADDITION OF THE RESIDUE SEQUENCE DL AS A RESULT OF CLONING

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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: 3.53 Å3/Da / Density % sol: 65.19 %
Description: SBGRID WIDE SEARCH MOLECULAR REPLACEMENT WSMR, STOKES-REES ET AL 2010, WAS USED AND THE STRUCTURE WAS SOLVED BY USING PHASER WITH THE FOLLOWING ENTRIES 2J00 - CHAIN C, N-TERMINAL DOMAIN 1MJ0A
Crystal growDetails: 0.1 M MES PH 6.0, 200 MM LITHIUM SULPHATE, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→34.57 Å / Num. obs: 12331 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 8.19130646 % / Biso Wilson estimate: 76.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.85
Reflection shellResolution: 2.84→3.01 Å / Redundancy: 8.41671018 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.86 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J00

2j00
PDB Unreleased entry


Resolution: 2.842→34.574 Å / SU ML: 0.4 / σ(F): 2 / Phase error: 23.53 / Stereochemistry target values: ML
Details: ABSENT REGIONS INCLUDE THE C-TERMINUS OF RPS3 AND THE C-TERMINUS OF YAR1
RfactorNum. reflection% reflection
Rfree0.2245 616 5 %
Rwork0.1891 --
obs0.1908 12328 94.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.5 Å2
Refinement stepCycle: LAST / Resolution: 2.842→34.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 0 0 2629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062667
X-RAY DIFFRACTIONf_angle_d0.9153597
X-RAY DIFFRACTIONf_dihedral_angle_d13.653996
X-RAY DIFFRACTIONf_chiral_restr0.067412
X-RAY DIFFRACTIONf_plane_restr0.004468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8419-3.12780.33181510.27562885X-RAY DIFFRACTION95
3.1278-3.580.24671530.22082901X-RAY DIFFRACTION95
3.58-4.50880.221550.17872939X-RAY DIFFRACTION95
4.5088-34.57630.19971570.16822987X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9035-0.15021.22533.50260.44764.4407-0.508-0.6609-0.39781.12840.5740.00880.52750.3616-0.00111.30010.33420.06790.9142-0.00580.802220.7193-36.939-3.9994
23.3962-0.9416-0.89873.310312.3653-0.050.5262-0.0156-0.6397-0.0381-0.18680.0349-0.1593-0.00020.5924-0.01580.09350.5248-0.00380.55747.2951-7.6953-14.5389
34.2697-1.9181-1.24493.1839-0.99182.6791-0.02680.7133-0.7223-0.24280.0291-0.28940.15940.2403-0.00040.5104-0.04510.10240.6075-0.06080.5243-10.1065.36554.4691
45.9589-3.6587-1.16253.53051.92953.27050.24120.0477-0.541-0.187-0.1626-0.12290.2220.1158-0.00530.78140.10740.09470.593-0.15680.615224.4394-41.0257-31.7653
51.82-2.0014-0.64054.98841.36092.22160.2640.3439-0.372-0.2051-0.3610.5294-0.0692-0.13460.00140.7040.08820.08720.5575-0.17250.685212.5376-26.9072-25.361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 12 THROUGH 91)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 92 THROUGH 159)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 160 THROUGH 198)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 7 THROUGH 75)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 76 THROUGH 156)

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