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- PDB-3rfh: Crystal structure of the yeast RACK1 dimer in space group P21 -

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Basic information

Entry
Database: PDB / ID: 3rfh
TitleCrystal structure of the yeast RACK1 dimer in space group P21
ComponentsGuanine nucleotide-binding protein subunit beta-like protein
KeywordsSIGNALING PROTEIN / beta-propeller / dimer
Function / homology
Function and homology information


negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / mRNA destabilization / G-protein alpha-subunit binding / translation regulator activity / rescue of stalled ribosome / protein kinase C binding / ribosome binding ...negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / mRNA destabilization / G-protein alpha-subunit binding / translation regulator activity / rescue of stalled ribosome / protein kinase C binding / ribosome binding / cytosolic small ribosomal subunit / cytoplasmic translation / negative regulation of translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / nucleus / cytoplasm / cytosol
Similarity search - Function
Small (40S) ribosomal subunit Asc1/RACK1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat ...Small (40S) ribosomal subunit Asc1/RACK1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Small ribosomal subunit protein RACK1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsYatime, L. / Hein, K.L. / Nilsson, J. / Nissen, P.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure of the RACK1 dimer from Saccharomyces cerevisiae
Authors: Yatime, L. / Hein, K.L. / Nilsson, J. / Nissen, P.
History
DepositionApr 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: 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 / 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
A: Guanine nucleotide-binding protein subunit beta-like protein
B: Guanine nucleotide-binding protein subunit beta-like protein
C: Guanine nucleotide-binding protein subunit beta-like protein
D: Guanine nucleotide-binding protein subunit beta-like protein


Theoretical massNumber of molelcules
Total (without water)138,8364
Polymers138,8364
Non-polymers00
Water68538
1
A: Guanine nucleotide-binding protein subunit beta-like protein
C: Guanine nucleotide-binding protein subunit beta-like protein


Theoretical massNumber of molelcules
Total (without water)69,4182
Polymers69,4182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-6 kcal/mol
Surface area24740 Å2
MethodPISA
2
B: Guanine nucleotide-binding protein subunit beta-like protein
D: Guanine nucleotide-binding protein subunit beta-like protein


Theoretical massNumber of molelcules
Total (without water)69,4182
Polymers69,4182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-6 kcal/mol
Surface area25470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.010, 165.650, 92.150
Angle α, β, γ (deg.)90.000, 98.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1


Mass: 34708.973 Da / Num. of mol.: 4 / Mutation: K283A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: ASC1, CPC2, YM9718.15C, YMR116C / Plasmid: pET46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P38011
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% polyacrylic acid 5100, 0.05M KCl, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.072 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2007 / Details: Dynamically bendable mirror
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 26256 / Num. obs: 26256 / % possible obs: 99.9 % / Observed criterion σ(F): 2.88 / Observed criterion σ(I): 2.88 / Redundancy: 4.5 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.145 / Net I/σ(I): 9.09
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.88 / Num. unique all: 2497 / Rsym value: 0.584 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RFG

3rfg


Resolution: 2.9→47.227 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8134 / SU ML: 0.41 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1557 5.93 %RANDOM
Rwork0.2149 ---
all0.2169 26252 --
obs0.2169 26252 99.9 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.273 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 125.88 Å2 / Biso mean: 50.7015 Å2 / Biso min: 15.24 Å2
Baniso -1Baniso -2Baniso -3
1-5.7458 Å2-0 Å2-13.5285 Å2
2---14.1242 Å2-0 Å2
3----1.007 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9068 0 0 38 9106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069268
X-RAY DIFFRACTIONf_angle_d0.97212609
X-RAY DIFFRACTIONf_chiral_restr0.0591443
X-RAY DIFFRACTIONf_plane_restr0.0051588
X-RAY DIFFRACTIONf_dihedral_angle_d14.7283223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9-2.99360.34881240.291822312355
2.9936-3.10060.3021380.278422922430
3.1006-3.22470.32371620.259321702332
3.2247-3.37140.27011450.242522562401
3.3714-3.54910.2621400.224822352375
3.5491-3.77140.31221330.242922292362
3.7714-4.06240.22611460.204822622408
4.0624-4.4710.17551270.171222642391
4.471-5.11730.18811580.158422242382
5.1173-6.44460.241370.216922472384
6.4446-47.23280.24921470.209122852432

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