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- PDB-9qeu: Structure of CHIP E3 ubiquitin ligase TPR domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9qeu
TitleStructure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 1
ComponentsE3 ubiquitin-protein ligase CHIP
KeywordsLIGASE / E3 ligase
Function / homology
Function and homology information


positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / negative regulation of vascular associated smooth muscle contraction / negative regulation of peroxisome proliferator activated receptor signaling pathway / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of smooth muscle cell apoptotic process / positive regulation of mitophagy / ERBB2 signaling pathway / negative regulation of cardiac muscle hypertrophy ...positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / negative regulation of vascular associated smooth muscle contraction / negative regulation of peroxisome proliferator activated receptor signaling pathway / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of smooth muscle cell apoptotic process / positive regulation of mitophagy / ERBB2 signaling pathway / negative regulation of cardiac muscle hypertrophy / nuclear inclusion body / misfolded protein binding / cellular response to misfolded protein / protein folding chaperone complex / RIPK1-mediated regulated necrosis / ubiquitin-ubiquitin ligase activity / chaperone-mediated autophagy / SMAD binding / TPR domain binding / negative regulation of smooth muscle cell apoptotic process / R-SMAD binding / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteolysis / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / protein autoubiquitination / Downregulation of TGF-beta receptor signaling / ERAD pathway / heat shock protein binding / positive regulation of protein ubiquitination / Hsp70 protein binding / response to ischemia / Regulation of TNFR1 signaling / Hsp90 protein binding / Regulation of necroptotic cell death / negative regulation of transforming growth factor beta receptor signaling pathway / G protein-coupled receptor binding / Downregulation of ERBB2 signaling / Regulation of PTEN stability and activity / RING-type E3 ubiquitin transferase / regulation of protein stability / tau protein binding / kinase binding / Regulation of RUNX2 expression and activity / Z disc / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / MAPK cascade / protein-folding chaperone binding / cellular response to heat / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / cellular response to hypoxia / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / protein stabilization / DNA repair / ubiquitin protein ligase binding / enzyme binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / TPR repeat region circular profile. / TPR repeat profile. ...CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.353 Å
AuthorsBreed, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Discovery of Small-Molecule Ligands for the E3 Ligase STUB1/CHIP from a DNA-Encoded Library Screen.
Authors: Lucas, S.C.C. / Milbradt, A.G. / Breed, J. / De Genst, E. / Jackson, A. / Solovyeva, A. / Ackroyd, B. / Bauer, M.R. / Liu, J. / Longmire, D. / Petrovic, D. / Rivers, E.L. / Stubbs, C. / ...Authors: Lucas, S.C.C. / Milbradt, A.G. / Breed, J. / De Genst, E. / Jackson, A. / Solovyeva, A. / Ackroyd, B. / Bauer, M.R. / Liu, J. / Longmire, D. / Petrovic, D. / Rivers, E.L. / Stubbs, C. / Winlow, P. / Bazzaz, S. / Dickson, P. / Gikunju, D. / Guie, M.A. / Guilinger, J.P. / Hupp, C.D. / Jetson, R. / Keefe, A.D. / Nugai, K. / Yeoman, J.T.S. / Zhang, Y. / Feng, X. / Yu, D. / Phillips, C.
History
DepositionMar 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CHIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3094
Polymers14,6501
Non-polymers6603
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-22 kcal/mol
Surface area7210 Å2
Unit cell
Length a, b, c (Å)47.051, 74.569, 78.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein E3 ubiquitin-protein ligase CHIP / Antigen NY-CO-7 / CLL-associated antigen KW-8 / Carboxy terminus of Hsp70-interacting protein / ...Antigen NY-CO-7 / CLL-associated antigen KW-8 / Carboxy terminus of Hsp70-interacting protein / RING-type E3 ubiquitin transferase CHIP / STIP1 homology and U box-containing protein 1


Mass: 14649.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STUB1, CHIP, PP1131 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UNE7, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-A1I6K / ~{N}-[(1~{R},2~{R})-2-[[(1~{S})-1-(2-methoxyphenyl)-3-(methylamino)-3-oxidanylidene-propyl]carbamoyl]cyclopentyl]-4,5,6,7-tetrahydro-1~{H}-indazole-3-carboxamide


Mass: 467.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H33N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25-30% (w/v) PEG3350, 200mM magnesium chloride and 100mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→39.79 Å / Num. obs: 17924 / % possible obs: 92.6 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.4
Reflection shellResolution: 1.353→1.497 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 896 / CC1/2: 0.577

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Processing

Software
NameVersionClassification
XDSdata reduction
STARANISOdata scaling
BUSTER2.11.8 (24-FEB-2021)refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.353→39.79 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.107 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.096
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 915 5.11 %RANDOM
Rwork0.2141 ---
obs0.2152 17919 59 %-
Displacement parametersBiso mean: 18.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.8448 Å20 Å20 Å2
2--3.5364 Å20 Å2
3----1.6915 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.353→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1002 0 39 113 1154
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081061HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.781432HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d383SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes182HARMONIC5
X-RAY DIFFRACTIONt_it1061HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion15.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion132SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1140SEMIHARMONIC4
LS refinement shellResolution: 1.353→1.46 Å
RfactorNum. reflection% reflection
Rfree0.3005 -6.52 %
Rwork0.2865 373 -
obs--6.72 %
Refinement TLS params.Method: refined / Origin x: 5.6156 Å / Origin y: 21.2541 Å / Origin z: 8.5882 Å
111213212223313233
T-0.0832 Å2-0.003 Å20.006 Å2-0.0294 Å2-0.0058 Å2---0.0797 Å2
L0.5672 °2-0.1221 °20.406 °2-0.2045 °2-0.0076 °2--0.5866 °2
S0.0357 Å °-0.0402 Å °0.0188 Å °-0.017 Å °0.0062 Å °0.012 Å °-0.0105 Å °0.0212 Å °-0.0419 Å °
Refinement TLS groupSelection details: { A|* }

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