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- PDB-3rfg: Crystal structure of the yeast RACK1 dimer in space group P63 -

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Basic information

Entry
Database: PDB / ID: 3rfg
TitleCrystal structure of the yeast RACK1 dimer in space group P63
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 / nonfunctional rRNA decay / mRNA destabilization / regulation of amino acid metabolic process / G-protein alpha-subunit binding / translation regulator activity / rescue of stalled ribosome ...negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / mRNA destabilization / regulation of amino acid metabolic process / G-protein alpha-subunit binding / translation regulator activity / rescue of stalled ribosome / protein kinase C binding / maintenance of translational fidelity / 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 / cytosol / cytoplasm
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / Small (40S) ribosomal subunit Asc1/RACK1 / 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 ...YVTN repeat-like/Quinoprotein amine dehydrogenase / Small (40S) ribosomal subunit Asc1/RACK1 / 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: 3.9 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


Theoretical massNumber of molelcules
Total (without water)69,5342
Polymers69,5342
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-6 kcal/mol
Surface area25590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.440, 177.440, 67.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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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: 34767.074 Da / Num. of mol.: 2
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

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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: 4.44 Å3/Da / Density % sol: 72.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM HEPES, 1.4M Ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 26, 2008 / Details: Dynamically bendable mirror
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
ReflectionResolution: 3.9→60 Å / Num. all: 11333 / Num. obs: 11333 / % possible obs: 99.55 % / Observed criterion σ(F): 3.3 / Observed criterion σ(I): 3.3 / Redundancy: 4.1 % / Biso Wilson estimate: 104 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.107 / Net I/σ(I): 12.03
Reflection shellResolution: 3.9→4 Å / Redundancy: 3.72 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.29 / Num. unique all: 814 / Rsym value: 0.441 / % possible all: 98.1

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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 3DM0

3dm0


Resolution: 3.9→58.081 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.835 / SU ML: 0.55 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 638 5.63 %RANDOM
Rwork0.2188 ---
all0.2209 11325 --
obs0.2209 11325 99.52 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.46 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso max: 226.61 Å2 / Biso mean: 119.1823 Å2 / Biso min: 54.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.2664 Å20 Å20 Å2
2---0.2664 Å20 Å2
3---1.697 Å2
Refinement stepCycle: LAST / Resolution: 3.9→58.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4444 0 0 0 4444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074542
X-RAY DIFFRACTIONf_angle_d1.1866178
X-RAY DIFFRACTIONf_chiral_restr0.07708
X-RAY DIFFRACTIONf_plane_restr0.003776
X-RAY DIFFRACTIONf_dihedral_angle_d15.2691578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9004-4.20140.2961200.23672120224099
4.2014-4.62410.22861300.190221012231100
4.6241-5.29280.21311340.183521282262100
5.2928-6.66680.25451370.241321282265100
6.6668-58.08730.28651170.23282210232799

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