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- PDB-7qqy: yeast Gid10 bound to Art2 Pro/N-degron -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7qqy
Titleyeast Gid10 bound to Art2 Pro/N-degron
Components
  • ECM21
  • Uncharacterized protein YGR066C
KeywordsLIGASE / GID / Art2 / ubiquitin / E3 ligase / metabolism
Function / homology
Function and homology information


protein catabolic process in the vacuole / GID complex / protein targeting to vacuole / vacuole / response to osmotic stress / extrinsic component of membrane / response to starvation / negative regulation of gluconeogenesis / protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process
Similarity search - Function
Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein
Similarity search - Domain/homology
Uncharacterized protein YGR066C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsChrustowicz, J. / Sherpa, D. / Schulman, B.A.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3196/1European Union
European Research Council (ERC)789016-NEDD8ActivateEuropean Union
CitationJournal: Embo Rep. / Year: 2022
Title: A GID E3 ligase assembly ubiquitinates an Rsp5 E3 adaptor and regulates plasma membrane transporters.
Authors: Langlois, C.R. / Beier, V. / Karayel, O. / Chrustowicz, J. / Sherpa, D. / Mann, M. / Schulman, B.A.
History
DepositionJan 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 15, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YGR066C
B: ECM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2283
Polymers27,1922
Non-polymers351
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.524, 67.817, 75.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Uncharacterized protein YGR066C


Mass: 26188.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YGR066C / Production host: Escherichia coli (E. coli) / References: UniProt: P53242
#2: Protein/peptide ECM21


Mass: 1004.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.91 Å3/Da / Density % sol: 35.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 18.5% PEG3350, 0.1 M Bis-Tris propane pH 6.0 and 0.2 M potassium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→40.52 Å / Num. obs: 57128 / % possible obs: 99.2 % / Redundancy: 12.6 % / CC1/2: 1 / Net I/σ(I): 26.1
Reflection shellResolution: 1.26→1.33 Å / Num. unique obs: 8755 / CC1/2: 0.9 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NS3

7ns3


Resolution: 1.26→37.74 Å / SU ML: 0.2047 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6053
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.227 2854 5.01 %
Rwork0.1918 54144 -
obs0.1936 56998 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.92 Å2
Refinement stepCycle: LAST / Resolution: 1.26→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 1 217 2039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591917
X-RAY DIFFRACTIONf_angle_d0.96532615
X-RAY DIFFRACTIONf_chiral_restr0.0975273
X-RAY DIFFRACTIONf_plane_restr0.0067335
X-RAY DIFFRACTIONf_dihedral_angle_d23.0962257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.280.5361220.55962292X-RAY DIFFRACTION85.54
1.28-1.30.38051420.41432706X-RAY DIFFRACTION99.68
1.3-1.330.38881400.36182653X-RAY DIFFRACTION99.96
1.33-1.350.42811440.35412719X-RAY DIFFRACTION99.83
1.35-1.380.37141400.36782677X-RAY DIFFRACTION99.86
1.38-1.410.40551420.40992695X-RAY DIFFRACTION100
1.41-1.450.41161430.3772717X-RAY DIFFRACTION99.97
1.45-1.490.34051420.29822694X-RAY DIFFRACTION99.93
1.49-1.530.28281420.25882705X-RAY DIFFRACTION100
1.53-1.580.2591430.22192715X-RAY DIFFRACTION100
1.58-1.640.23451430.20422706X-RAY DIFFRACTION99.96
1.64-1.70.22711440.19312726X-RAY DIFFRACTION100
1.7-1.780.21781430.17572718X-RAY DIFFRACTION99.93
1.78-1.880.20051430.16572714X-RAY DIFFRACTION100
1.88-1.990.16451450.16482755X-RAY DIFFRACTION100
1.99-2.150.18591440.16372736X-RAY DIFFRACTION100
2.15-2.360.21911460.16622770X-RAY DIFFRACTION100
2.36-2.710.19181460.17442765X-RAY DIFFRACTION100
2.71-3.410.1911470.16562806X-RAY DIFFRACTION99.97
3.41-37.740.24071530.17332875X-RAY DIFFRACTION97.93

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