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- PDB-7u3j: GID4 in complex with compound 88 -

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Basic information

Entry
Database: PDB / ID: 7u3j
TitleGID4 in complex with compound 88
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-L6U / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.642 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)20,3284
Polymers19,6051
Non-polymers7233
Water2,018112
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)40.350, 58.530, 69.100
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) / Variant (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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-L6U / (2S)-2-{[(2S)-2-({N-[(2,4-dimethoxyphenyl)methyl]glycyl}amino)-2-(thiophen-2-yl)acetyl]amino}-N-methyl-4-phenylbutanamide


Mass: 538.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H34N4O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 18% PEG6000, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.64→44.662 Å / Num. obs: 20341 / % possible obs: 98.7 % / Redundancy: 7.332 % / Biso Wilson estimate: 29.482 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.085 / Χ2: 0.795 / Net I/σ(I): 15.58 / Num. measured all: 149139
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
1.64-1.746.1710.9391.9818599327730140.7661.02392
1.74-1.857.820.5334.4923968306630650.9520.57100
1.85-27.7120.2878.222280289028890.9820.308100
2-2.197.2780.16512.3519271264926480.9920.178100
2.19-2.457.9770.11518.0319256241424140.9950.122100
2.45-2.837.6230.08323.0116457216121590.9970.0999.9
2.83-3.467.0970.05531.3513001183418320.9980.05999.9
3.46-4.887.3540.04339.5710670145114510.9990.046100
4.88-44.6626.4870.04137.6156378718690.9980.04499.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.93 Å44.66 Å
Translation3.93 Å44.66 Å

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDS20210322data reduction
XSCALE20210322data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CCR

6ccr


Resolution: 1.642→44.662 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2023 1016 5 %
Rwork0.1831 19306 -
obs0.1841 20322 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.61 Å2 / Biso mean: 32.3683 Å2 / Biso min: 16.03 Å2
Refinement stepCycle: final / Resolution: 1.642→44.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 65 112 1519
Biso mean--39.74 39.03 -
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 (%)
1.6423-1.72890.35991300.3367248591
1.7289-1.83720.25911450.25482767100
1.8372-1.97910.22781450.19212738100
1.9791-2.17820.21450.18512756100
2.1782-2.49340.21661470.17822786100
2.4934-3.14130.18651480.18022821100
3.1413-44.6620.18281560.16242953100
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)
12.0165.6861-6.49624.6865-3.48226.0161-0.25110.00420.21-0.00210.09950.00720.17230.11730.08640.2060.001-0.01620.21540.00170.17829.37730.24713.7563
27.64086.09883.46999.37013.45473.0271-0.1302-0.02590.5393-0.06-0.02730.2921-0.18620.00450.15610.13010.01490.01870.16240.02530.13192.72242.3609-2.3237
37.12553.3454-4.30282.0205-5.40362.0434-0.07441.1230.1705-0.89350.51690.494-0.1897-0.5026-0.44240.4233-0.0243-0.00340.38080.00180.20645.9783-11.3669-16.4278
47.07910.79732.18189.1134-5.12468.5640.04240.0287-0.2852-0.46910.01-0.34740.46510.2605-0.04510.14150.0183-0.00450.1482-0.02880.162315.039-14.4692-9.0868
52.00636.1083-6.48078.3399-4.16122.0028-0.61590.4797-0.4271-0.119-0.1408-0.55940.23040.07550.79730.44360.0016-0.07510.46280.0260.48479.4308-22.9268-13.0213
61.62620.40940.04275.2445-1.12341.24180.02320.06260.1787-0.0468-0.0040.0225-0.09830.0199-0.01860.12560.00760.02180.16390.00460.1267.5449-3.8417-5.0836
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 179 )A137 - 179
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 194 )A180 - 194
4X-RAY DIFFRACTION4chain 'A' and (resid 195 through 210 )A195 - 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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