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- PDB-9r1p: Crystal structure of STUB1 complexed with a compound molecule -

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Basic information

Entry
Database: PDB / ID: 9r1p
TitleCrystal structure of STUB1 complexed with a compound molecule
ComponentsE3 ubiquitin-protein ligase CHIP
KeywordsCELL CYCLE / STIP1 homology and U-Box containing protein 1 / E3 ubiquitin 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 / R-SMAD binding / negative regulation of smooth muscle cell apoptotic process / 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 / Regulation of TNFR1 signaling / response to ischemia / 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: 2.29 Å
AuthorsChu, Y. / Jiang, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Biotechnol. / Year: 2025
Title: A rapid imaging-based screen for induced-proximity degraders identifies a potent degrader of oncoprotein SKP2.
Authors: Chu, Y. / Chen, S. / Yang, M. / Chen, Y. / Fang, H. / Huang, P. / Xie, Y. / Sun, C. / Chen, Y. / Zhang, B. / Li, L. / Mu, H. / Song, D. / Cheng, W. / Wang, C. / Jiang, W. / Xu, X. / He, Z. / ...Authors: Chu, Y. / Chen, S. / Yang, M. / Chen, Y. / Fang, H. / Huang, P. / Xie, Y. / Sun, C. / Chen, Y. / Zhang, B. / Li, L. / Mu, H. / Song, D. / Cheng, W. / Wang, C. / Jiang, W. / Xu, X. / He, Z. / Chen, S. / Liu, M. / Ma, J. / Yang, M. / Cao, J. / Gao, J. / Shen, J. / Zhang, L. / Bai, Y. / Liu, Z. / Chen, J. / Dai, S. / Zeng, Y.A. / Zhao, Y. / Zhou, H. / Chen, C. / Ru, H. / Tan, L. / Chi, X. / Wang, F. / Gao, D. / Lin, M. / Deng, X. / Jiang, H.
History
DepositionApr 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 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)16,3272
Polymers15,7931
Non-polymers5351
Water1086
1
A: E3 ubiquitin-protein ligase CHIP
hetero molecules

A: E3 ubiquitin-protein ligase CHIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6554
Polymers31,5862
Non-polymers1,0692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2470 Å2
ΔGint-12 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.948, 89.948, 53.597
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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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: 15792.862 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-A1JBJ / 1-[3-[1-methyl-4-(pyridin-3-ylmethylamino)pyrazolo[3,4-d]pyrimidin-6-yl]phenyl]-3-[3-(trifluoromethyl)phenyl]thiourea


Mass: 534.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H21F3N8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.96 Å3/Da / Density % sol: 68.96 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 20% PEG4000,pH7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Nov 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.29→44.97 Å / Num. obs: 11510 / % possible obs: 99.7 % / Redundancy: 20.3 % / Biso Wilson estimate: 48.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.013 / Rrim(I) all: 0.06 / Net I/σ(I): 28.3
Reflection shellResolution: 2.29→2.41 Å / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 7.7 / Num. unique obs: 1626 / CC1/2: 0.993 / Rpim(I) all: 0.066 / Rrim(I) all: 0.304

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→44.97 Å / SU ML: 0.2242 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.5227
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2339 537 4.68 %
Rwork0.2052 10928 -
obs0.2067 11465 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.39 Å2
Refinement stepCycle: LAST / Resolution: 2.29→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 38 6 1024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541038
X-RAY DIFFRACTIONf_angle_d0.88211398
X-RAY DIFFRACTIONf_chiral_restr0.0349141
X-RAY DIFFRACTIONf_plane_restr0.0049183
X-RAY DIFFRACTIONf_dihedral_angle_d11.9553143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.520.23781560.24572625X-RAY DIFFRACTION97.99
2.52-2.890.2941170.23022723X-RAY DIFFRACTION99.72
2.89-3.640.3351230.25782749X-RAY DIFFRACTION99.86
3.64-44.970.18731410.17012831X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -32.8650398159 Å / Origin y: 31.5947415877 Å / Origin z: 10.3568307927 Å
111213212223313233
T0.379409373207 Å20.0061680300117 Å2-0.014936064612 Å2-0.444130758628 Å20.0273439121043 Å2--0.544674391076 Å2
L2.6686919386 °22.1361285202 °2-0.300601192796 °2-5.36459803255 °21.02091862867 °2--2.52359922191 °2
S-0.0471131844706 Å °-0.111450535319 Å °-0.272538352119 Å °0.154617808244 Å °-0.0154751188157 Å °-0.169804749218 Å °0.33284692279 Å °0.0755760939064 Å °0.0275768733055 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection details: all / Auth asym-ID: A

IDLabel asym-IDAuth seq-IDLabel seq-ID
1A23 - 14510 - 132
2B201
3C301 - 306

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