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- PDB-3frx: Crystal Structure of the Yeast Orthologue of RACK1, Asc1. -

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Basic information

Entry
Database: PDB / ID: 3frx
TitleCrystal Structure of the Yeast Orthologue of RACK1, Asc1.
ComponentsGuanine nucleotide-binding protein subunit beta-like protein
KeywordsSIGNALING PROTEIN / RACK1 / WD40 / BETA PROPELLER / RIBOSOME / TRANSLATION / Acetylation / Cytoplasm / Phosphoprotein / WD repeat
Function / homology
Function and homology information


regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / mRNA destabilization / negative regulation of translational frameshifting / G-protein alpha-subunit binding / translation regulator activity / rescue of stalled ribosome ...regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / mRNA destabilization / negative regulation of translational frameshifting / 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 / 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 / WD domain, G-beta repeat / 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. ...Small (40S) ribosomal subunit Asc1/RACK1 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / 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. / 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 / Resolution: 2.13 Å
AuthorsCoyle, S.M. / Gilbert, W.V. / Doudna, J.A.
CitationJournal: Mol.Cell.Biol. / Year: 2009
Title: Direct link between RACK1 function and localization at the ribosome in vivo
Authors: Coyle, S.M. / Gilbert, W.V. / Doudna, J.A.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,8988
Polymers140,6784
Non-polymers2204
Water25,9061438
1
A: Guanine nucleotide-binding protein subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2242
Polymers35,1691
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Guanine nucleotide-binding protein subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2242
Polymers35,1691
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Guanine nucleotide-binding protein subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2242
Polymers35,1691
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Guanine nucleotide-binding protein subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2242
Polymers35,1691
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)168.660, 85.410, 119.100
Angle α, β, γ (deg.)90.00, 134.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-904-

HOH

21C-970-

HOH

31C-1018-

HOH

41D-754-

HOH

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Components

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


Mass: 35169.480 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ASC1, CPC2, YM9718.15C, YMR116C / Plasmid: pSV272 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38011
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1438 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 13.3% PEG 2000 MME, 22 mM MnOAc, 100 mM NaOAc, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9793713 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793713 Å / Relative weight: 1
ReflectionResolution: 2.13→17.519 Å / Num. all: 204852 / Num. obs: 125144
Reflection shellResolution: 2.13→2.1569 Å / Num. unique all: 125144 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→17.519 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 1.2 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 3796 3.03 %
Rwork0.195 --
obs0.196 125144 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.049 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 195.39 Å2 / Biso mean: 26.659 Å2 / Biso min: 1.47 Å2
Baniso -1Baniso -2Baniso -3
1--3.121 Å20 Å2-0.355 Å2
2--3.696 Å2-0 Å2
3----0.576 Å2
Refinement stepCycle: LAST / Resolution: 2.13→17.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9552 0 4 1438 10994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.15690.31141530.26914616X-RAY DIFFRACTION98
2.1569-2.18530.29481470.27014569X-RAY DIFFRACTION98
2.1853-2.21510.29941280.25854608X-RAY DIFFRACTION97
2.2151-2.24670.25941480.24684670X-RAY DIFFRACTION97
2.2467-2.28020.28551520.24244541X-RAY DIFFRACTION97
2.2802-2.31570.27581290.23744666X-RAY DIFFRACTION97
2.3157-2.35360.30691380.24024571X-RAY DIFFRACTION97
2.3536-2.39410.3271400.24054543X-RAY DIFFRACTION97
2.3941-2.43750.25891550.22934575X-RAY DIFFRACTION97
2.4375-2.48430.29251340.2284609X-RAY DIFFRACTION97
2.4843-2.53480.3021480.23244463X-RAY DIFFRACTION96
2.5348-2.58980.27021460.23564556X-RAY DIFFRACTION96
2.5898-2.64980.23771380.21924566X-RAY DIFFRACTION96
2.6498-2.71590.2161330.20634507X-RAY DIFFRACTION96
2.7159-2.7890.24381540.20264496X-RAY DIFFRACTION95
2.789-2.87070.34811420.21344489X-RAY DIFFRACTION95
2.8707-2.9630.28981440.21134508X-RAY DIFFRACTION95
2.963-3.06830.21971320.19334486X-RAY DIFFRACTION94
3.0683-3.19050.24831390.17834371X-RAY DIFFRACTION94
3.1905-3.33470.19271330.17024495X-RAY DIFFRACTION94
3.3347-3.50920.17711310.16174406X-RAY DIFFRACTION93
3.5092-3.72710.18681460.15164324X-RAY DIFFRACTION92
3.7271-4.01170.20171350.15054356X-RAY DIFFRACTION92
4.0117-4.40960.16991260.13294350X-RAY DIFFRACTION92
4.4096-5.03440.15071440.12574318X-RAY DIFFRACTION91
5.0344-6.29350.22781420.16254348X-RAY DIFFRACTION92
6.2935-17.51950.20741390.19114341X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 83.6727 Å / Origin y: 9.6898 Å / Origin z: 21.8169 Å
111213212223313233
T0.0226 Å20.0112 Å2-0.0006 Å2-0.0131 Å2-0.0001 Å2--0.0351 Å2
L0.0696 °20.0009 °20.0039 °2--0.0032 °20.0024 °2--0.002 °2
S0.0107 Å °-0.0075 Å °-0.0155 Å °0.0021 Å °0.0006 Å °-0.0034 Å °-0.001 Å °0.0005 Å °-0.0113 Å °
Refinement TLS groupSelection details: all

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