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- PDB-7u3i: GID4 in complex with compound 16 -

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Basic information

Entry
Database: PDB / ID: 7u3i
TitleGID4 in complex with compound 16
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-L5X / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.991 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: Glucose-induced degradation protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8106
Polymers39,2102
Non-polymers6014
Water1,18966
1
A: Glucose-induced degradation protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9053
Polymers19,6051
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-induced degradation protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9053
Polymers19,6051
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.651, 40.141, 51.614
Angle α, β, γ (deg.)89.990, 107.900, 89.970
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 124 through 128 or (resid 129...
21(chain B and (resid 124 through 145 or (resid 146...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPHEPHE(chain A and (resid 124 through 128 or (resid 129...AA124 - 1282 - 6
12ARGARGARGARG(chain A and (resid 124 through 128 or (resid 129...AA1297
13SERSERVALVAL(chain A and (resid 124 through 128 or (resid 129...AA124 - 2892 - 167
14SERSERVALVAL(chain A and (resid 124 through 128 or (resid 129...AA124 - 2892 - 167
15SERSERVALVAL(chain A and (resid 124 through 128 or (resid 129...AA124 - 2892 - 167
16SERSERVALVAL(chain A and (resid 124 through 128 or (resid 129...AA124 - 2892 - 167
17SERSERVALVAL(chain A and (resid 124 through 128 or (resid 129...AA124 - 2892 - 167
18SERSERVALVAL(chain A and (resid 124 through 128 or (resid 129...AA124 - 2892 - 167
21SERSERLEULEU(chain B and (resid 124 through 145 or (resid 146...BB124 - 1452 - 23
22GLNGLNHISHIS(chain B and (resid 124 through 145 or (resid 146...BB146 - 14724 - 25
23SERSERVALVAL(chain B and (resid 124 through 145 or (resid 146...BB124 - 2892 - 167
24SERSERVALVAL(chain B and (resid 124 through 145 or (resid 146...BB124 - 2892 - 167
25SERSERVALVAL(chain B and (resid 124 through 145 or (resid 146...BB124 - 2892 - 167
26SERSERVALVAL(chain B and (resid 124 through 145 or (resid 146...BB124 - 2892 - 167
27SERSERVALVAL(chain B and (resid 124 through 145 or (resid 146...BB124 - 2892 - 167

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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.: 2
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-L5X / 3-{[(5S)-5-methyl-4,5-dihydro-1,3-thiazol-2-yl]amino}phenol


Mass: 208.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.94 Å3/Da / Density % sol: 36.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% 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-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.99→49.116 Å / Num. obs: 18720 / % possible obs: 98.3 % / Redundancy: 3.318 % / Biso Wilson estimate: 43.269 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.091 / Χ2: 0.768 / Net I/σ(I): 9.81
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
1.99-2.113.1330.9481.324969167315860.5331.13894.8
2.11-2.253.2990.6112.225116158115510.770.72998.1
2.25-2.433.4780.4063.485081147014610.8940.48199.4
2.43-2.663.3890.2475.454582135413520.9510.29499.9
2.66-2.983.3140.1348.974050123712220.9850.16198.8
2.98-3.443.2940.06915.653561109310810.9940.08298.9
3.44-4.23.4410.04423.7432079359320.9970.05299.7
4.2-5.923.2240.03628.9222897287100.9970.04397.5
5.92-49.1163.2690.03229.9813864314240.9980.03898.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.1 Å49.12 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: 1.991→49.116 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 943 5.04 %
Rwork0.1961 17777 -
obs0.1979 18720 92.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.71 Å2 / Biso mean: 49.2145 Å2 / Biso min: 22.74 Å2
Refinement stepCycle: final / Resolution: 1.991→49.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 40 66 2531
Biso mean--59.58 47.28 -
Num. residues----308
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1333X-RAY DIFFRACTION7.211TORSIONAL
12B1333X-RAY DIFFRACTION7.211TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.991-2.09550.36271150.322232985
2.0955-2.22680.32821350.287246189
2.2268-2.39870.30081410.2513260295
2.3987-2.64010.31211380.2362258995
2.6401-3.02210.231330.2018256293
3.0221-3.80730.19271370.1762261495
3.8073-49.1160.19951440.1626262095
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)
14.4135-3.3121.40085.6124-2.34964.3384-0.36040.13850.2457-0.43320.33360.2994-0.3112-0.4582-0.05660.3562-0.0411-0.11410.41950.03440.367-8.1935-2.654-14.6583
26.7035-3.79812.93756.1995-1.89877.43770.63760.8988-0.1497-1.2347-0.38460.52150.53510.168-0.21690.4808-0.0382-0.03010.3180.01050.2963-2.4217-7.5913-17.7162
33.9450.7415-0.62390.24220.22053.27320.09830.31780.1078-0.79020.1021-1.27730.27690.4395-0.08530.28660.0310.17090.4001-0.00790.749913.5449-2.3745-9.6974
49.89262.6659-3.62792.3518-1.29552.172-0.06280.56220.39230.46780.1226-1.1007-0.87480.0751-0.01730.5321-0.02290.05890.35930.00640.48939.49467.1633-7.9022
55.4392-2.7907-2.17082.0383-0.9498.6685-0.2534-0.6065-0.08410.2310.8712-0.97290.27190.8787-0.56090.46320.0346-0.02910.4759-0.06870.53547.00113.0382.8263
65.159-5.0596-0.87085.2352.41128.145-0.6516-2.5428-0.40661.30891.2954-0.32170.06531.4206-0.48040.69220.1087-0.03240.69140.08660.51535.9626-5.79074.9002
72.94461.29270.67476.47885.65976.90820.07770.2152-0.3048-0.61290.3425-0.3007-0.99350.3534-0.41520.36330.01820.0450.28290.03080.31752.5991-4.6591-13.1193
83.1854-0.16470.0222.3936-0.23553.94090.16980.4310.2909-0.41370.0035-0.0873-0.5006-0.0978-0.13040.3653-0.02730.02340.29730.05280.2971-1.0286-1.012-14.3691
97.6903-1.7798-1.89446.52561.32496.23940.16730.43281.6653-0.90260.11950.0513-0.87980.0627-0.23950.49870.03930.04650.50180.0760.3721-0.93434.9601-14.8379
105.99742.71262.76645.39373.72146.7321-0.1861-0.34680.43210.5280.4787-0.1947-0.31840.1612-0.29010.4494-0.0109-0.10450.492-0.0070.52167.95419.762112.4462
117.3114.84663.37499.05523.30225.63890.0237-0.54-0.42670.7476-0.0126-0.39510.12930.1241-0.05340.3680.056-0.02640.4090.03060.35882.233412.350612.5905
122.51410.1540.44855.9080.29775.2088-0.0598-0.31871.66612.5994-1.9655-0.34150.9115-0.36151.37320.9022-0.2876-0.19590.9849-0.00150.645113.032820.462725.9939
131.8222-0.60572.32935.8512-0.83614.2645-0.1561-0.34530.14370.27730.15240.7509-0.4997-0.4241-0.04260.311-0.00270.11560.35640.02570.4135-10.228819.0569.5934
142.6386-2.9323-1.68245.55730.15672.34510.17780.4407-0.5334-0.73520.78291.44820.0763-1.1534-0.92430.5099-0.093-0.02670.55820.1560.6237-8.243823.1022-4.4671
154.21124.179-0.43574.1742-0.90136.1895-0.36382.56820.5881-1.4780.86090.1665-0.0654-0.5482-0.51840.6057-0.14430.01930.55070.00920.4775-7.32214.4519-6.4366
164.64160.41.98172.9873-0.3058.130.1748-0.6394-0.23410.7320.14240.03190.1132-0.405-0.31470.46660.00250.03050.24050.00210.2861-1.407414.578416.4563
175.5662-0.0606-1.61595.2931-0.00584.47780.3251-0.63110.61570.5575-0.00110.056-0.80490.0998-0.38470.42240.00530.03560.3014-0.00550.3106-0.94122.327710.8408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 124 through 149 )A124 - 149
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 179 )A150 - 179
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 194 )A180 - 194
4X-RAY DIFFRACTION4chain 'A' and (resid 195 through 204 )A195 - 204
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 221 )A205 - 221
6X-RAY DIFFRACTION6chain 'A' and (resid 222 through 229 )A222 - 229
7X-RAY DIFFRACTION7chain 'A' and (resid 230 through 240 )A230 - 240
8X-RAY DIFFRACTION8chain 'A' and (resid 241 through 274 )A241 - 274
9X-RAY DIFFRACTION9chain 'A' and (resid 275 through 289 )A275 - 289
10X-RAY DIFFRACTION10chain 'B' and (resid 124 through 136 )B124 - 136
11X-RAY DIFFRACTION11chain 'B' and (resid 137 through 161 )B137 - 161
12X-RAY DIFFRACTION12chain 'B' and (resid 162 through 170 )B162 - 170
13X-RAY DIFFRACTION13chain 'B' and (resid 171 through 204 )B171 - 204
14X-RAY DIFFRACTION14chain 'B' and (resid 205 through 221 )B205 - 221
15X-RAY DIFFRACTION15chain 'B' and (resid 222 through 229 )B222 - 229
16X-RAY DIFFRACTION16chain 'B' and (resid 230 through 251 )B230 - 251
17X-RAY DIFFRACTION17chain 'B' and (resid 252 through 289 )B252 - 289

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