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- PDB-7u3f: GID4 in complex with compound 4 -

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Basic information

Entry
Database: PDB / ID: 7u3f
TitleGID4 in complex with compound 4
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 / Regulation of pyruvate metabolism / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cytosol / Chem-L5L / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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)19,9423
Polymers19,6051
Non-polymers3372
Water45025
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)40.340, 57.280, 72.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-L5L / (4R)-4-(4-methoxyphenyl)-4,5,6,7-tetrahydrothieno[3,2-c]pyridine


Mass: 245.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15NOS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 15% PEG5000 MME, 0.1 M Bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→44.952 Å / Num. obs: 7797 / % possible obs: 98.2 % / Redundancy: 5.872 % / Biso Wilson estimate: 51.704 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.089 / Χ2: 1.03 / Net I/σ(I): 13.54 / Num. measured all: 45787
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
2.3-2.433.6010.7571.524030125011190.7640.88789.5
2.43-2.65.5220.5892.876494118411760.9010.65199.3
2.6-2.816.7630.3725.347405109510950.9690.403100
2.81-3.086.5930.1939.356797103110310.990.21100
3.08-3.446.2260.10414.9657289219200.9960.11499.9
3.44-3.976.6440.06423.8454688248230.9980.06999.9
3.97-4.856.0670.04630.5543267147130.9980.0599.9
4.85-6.816.390.04631.7736685755740.9980.05199.8
6.81-44.9525.4080.04233.4618713483460.9980.04799.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.99 Å44.95 Å

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDS20190806data reduction
XSCALE20190806data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CCR

6ccr


Resolution: 2.3→44.952 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2618 392 5.06 %
Rwork0.2333 7358 -
obs0.2349 7750 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.56 Å2 / Biso mean: 57.1714 Å2 / Biso min: 32.56 Å2
Refinement stepCycle: final / Resolution: 2.3→44.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 23 25 1351
Biso mean--61.44 50.97 -
Num. residues----166
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.63280.3491120.3143231995
2.6328-3.31690.32321460.27292461100
3.3169-44.9520.22471340.20512578100
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)
15.8705-0.718-3.98386.77921.43258.30130.23280.28011.0886-0.26690.45390.1167-0.4326-0.4246-0.62760.5220.19120.02260.44520.09960.4813-8.00071.95-1.5173
25.9732-2.2401-0.84354.8014-0.05362.10490.0271-0.4080.7711-0.02430.1492-0.3431-0.07160.1071-0.13090.3565-0.0280.0150.4399-0.06130.3861-0.8536-0.79773.8605
34.8655-0.85521.21956.2-1.13043.889-0.0801-0.01591.07380.6792-0.1255-0.8541-0.7821-0.08370.16790.5713-0.10550.03150.5386-0.17320.576-4.34996.56367.5938
49.3049-1.7254-0.51053.9238-0.5195.4660.1806-1.0816-0.65380.41280.03950.35590.22250.0515-0.27760.3022-0.0539-0.01130.52360.02180.2957-11.8114-13.878912.4461
59.0806-2.6633.42133.498-4.02174.6301-0.4670.1401-1.52270.74910.69690.51640.4576-2.2213-0.18251.0924-0.114-0.20890.936-0.02060.8974-10.1846-24.410811.2119
64.46671.2689-0.72772.4963-0.11554.48510.2301-0.38040.57420.0631-0.0680.0681-0.31360.0244-0.17760.320.0048-0.00630.5308-0.1140.3824-7.9576-3.84467.2513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 124 through 136 )A124 - 136
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 162 )A137 - 162
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 179 )A163 - 179
4X-RAY DIFFRACTION4chain 'A' and (resid 180 through 210 )A180 - 210
5X-RAY DIFFRACTION5chain 'A' and (resid 211 through 221 )A211 - 221
6X-RAY DIFFRACTION6chain 'A' and (resid 222 through 289 )A222 - 289

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