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- PDB-7u3h: GID4 in complex with compound 7 -

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Basic information

Entry
Database: PDB / ID: 7u3h
TitleGID4 in complex with compound 7
ComponentsGlucose-induced degradation protein 4 homolog
KeywordsPEPTIDE BINDING PROTEIN/INHIBITOR / Complex / Inhibitor / Protein degradation / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-INHIBITOR complex
Function / homologyVacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / ubiquitin ligase complex / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Chem-L6O / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.798 Å
AuthorsChana, C.K. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-143277 Canada
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery and Structural Characterization of Small Molecule Binders of the Human CTLH E3 Ligase Subunit GID4.
Authors: Chana, C.K. / Maisonneuve, P. / Posternak, G. / Grinberg, N.G.A. / Poirson, J. / Ona, S.M. / Ceccarelli, D.F. / Mader, P. / St-Cyr, D.J. / Pau, V. / Kurinov, I. / Tang, X. / Deng, D. / Cui, ...Authors: Chana, C.K. / Maisonneuve, P. / Posternak, G. / Grinberg, N.G.A. / Poirson, J. / Ona, S.M. / Ceccarelli, D.F. / Mader, P. / St-Cyr, D.J. / Pau, V. / Kurinov, I. / Tang, X. / Deng, D. / Cui, W. / Su, W. / Kuai, L. / Soll, R. / Tyers, M. / Rost, H.L. / Batey, R.A. / Taipale, M. / Gingras, A.C. / Sicheri, F.
History
DepositionFeb 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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: Glucose-induced degradation protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8152
Polymers19,6051
Non-polymers2101
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.469, 40.534, 51.584
Angle α, β, γ (deg.)90.000, 107.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glucose-induced degradation protein 4 homolog / Vacuolar import and degradation protein 24 homolog


Mass: 19604.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Plasmid: PET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8IVV7
#2: Chemical ChemComp-L6O / (5R)-N-(4-fluorophenyl)-5-methyl-4,5-dihydro-1,3-thiazol-2-amine


Mass: 210.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11FN2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.798→49.08 Å / Num. obs: 13855 / % possible obs: 97.1 % / Redundancy: 3.486 % / Biso Wilson estimate: 35.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.062 / Χ2: 0.799 / Net I/σ(I): 13.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.913.0660.5871.766344228220690.7830.71290.7
1.91-2.043.630.323.937724215021280.9390.37599
2.04-2.23.6370.2046.327143198819640.9750.2498.8
2.2-2.413.4330.1388.816214187118100.9840.16496.7
2.41-2.73.6820.09313.156142167616680.9930.10999.5
2.7-3.113.6090.05719.975295148414670.9960.06798.9
3.11-3.813.4020.03529.794144125112180.9980.04297.4
3.81-5.373.5840.02739.7234989889760.9980.03298.8
5.37-49.083.2320.02638.1517945735550.9980.03196.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.74 Å49.08 Å
Translation3.74 Å49.08 Å

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDS20200417data reduction
XSCALE20200417data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CCR

6ccr


Resolution: 1.798→49.08 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 693 5 %
Rwork0.1821 13157 -
obs0.1842 13850 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.8 Å2 / Biso mean: 40.541 Å2 / Biso min: 16.32 Å2
Refinement stepCycle: final / Resolution: 1.798→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 14 86 1405
Biso mean--35.15 48.53 -
Num. residues----163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7983-1.93710.35081300.2628248092
1.9371-2.1320.3031400.2155265799
2.132-2.44060.24711380.1954262398
2.4406-3.07480.23571420.1923268399
3.0748-49.080.18561430.1597271498
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)
15.6191-0.33132.75914.5023-0.00914.8980.0150.25690.0478-0.44660.08670.0694-0.0731-0.0055-0.0960.23540.00310.06510.14830.01630.1320.8116-3.707-13.4385
29.8241-6.24574.17417.0138-6.21019.1182-0.2886-0.33730.21320.57240.2339-0.80720.01350.80820.0730.37930.0271-0.02470.3377-0.09180.30378.2033-1.2264.353
33.5239-0.1402-0.24663.78470.7845.76360.11630.39740.2164-0.4341-0.09690.1275-0.443-0.1005-0.01350.24290.01130.0040.1580.02330.20790.3303-1.0823-14.7739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 124 through 204 )A124 - 204
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 229 )A205 - 229
3X-RAY DIFFRACTION3chain 'A' and (resid 230 through 289 )A230 - 289

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