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- PDB-7u3l: GID4 in complex with compound 91 -

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Basic information

Entry
Database: PDB / ID: 7u3l
TitleGID4 in complex with compound 91
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-L4X / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.295 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)20,2103
Polymers19,6051
Non-polymers6052
Water54030
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)37.914, 40.558, 54.257
Angle α, β, γ (deg.)90.000, 109.900, 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-L4X / Nalpha-{(2R,4E)-2-[(N-benzylglycyl)amino]-5-phenylpent-4-enoyl}-N,4-dimethyl-L-phenylalaninamide


Mass: 512.643 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H36N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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 Å3/Da / Density % sol: 38.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2 M sodium fluoride

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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: 2.27→35.649 Å / Num. obs: 7057 / % possible obs: 97.7 % / Redundancy: 3.37 % / Biso Wilson estimate: 47.911 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.127 / Χ2: 0.751 / Net I/σ(I): 9.09 / Num. measured all: 23783
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
2.27-2.413.4050.9681.73650116410720.6071.14892.1
2.41-2.573.4640.742.373654106010550.7030.87799.5
2.57-2.783.4320.4663.72341810129960.8560.55398.4
2.78-3.043.1350.2555.429039369260.9450.30698.9
3.04-3.43.3930.1379.528848558500.9820.16299.4
3.4-3.913.5080.0815.0425647397310.9930.09498.9
3.91-4.783.3540.05121.8121776576490.9970.06198.8
4.78-6.73.1640.04521.1515414994870.9960.05497.6
6.7-35.6493.4090.035269922992910.9980.04297.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.29 Å35.65 Å
Translation2.29 Å35.65 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: 2.295→35.649 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 352 5.02 %
Rwork0.2336 6662 -
obs0.2348 7014 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.3 Å2 / Biso mean: 54.7661 Å2 / Biso min: 30.69 Å2
Refinement stepCycle: final / Resolution: 2.295→35.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 44 30 1325
Biso mean--55.34 50.04 -
Num. residues----162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2953-2.62730.3671170.32692198
2.6273-3.30980.26551150.27422201
3.3098-35.6490.21921200.19752263
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)
16.2151-1.8814-3.03613.6514-1.42534.10080.17270.25430.4163-0.1369-0.0972-0.2859-0.10440.0403-0.09750.2689-0.0652-0.0460.2364-0.04530.35193.29427.1881-16.3328
25.7852-3.77521.78454.4004-0.3452.2888-0.1027-0.2518-0.1230.46940.37620.71050.0793-0.2097-0.30030.47860.0090.06330.20210.09310.4265-10.6258-0.8687-4.1658
32.4846-0.79141.5083.0741.395.1651-0.00050.03420.03610.0311-0.0632-0.12210.1857-0.02730.10010.3932-0.02170.01630.16110.04060.3865-2.98972.6174-10.4834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 124 through 179 )A124 - 179
2X-RAY DIFFRACTION2chain 'A' and (resid 180 through 214 )A180 - 214
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 289 )A215 - 289

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