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- PDB-8ei0: Crystal structure of the STUB1 TPR domain in complex with H318, a... -

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Basic information

Entry
Database: PDB / ID: 8ei0
TitleCrystal structure of the STUB1 TPR domain in complex with H318, a Helicon Polypeptide
Components
  • E3 ubiquitin-protein ligase CHIP
  • H318
KeywordsLIGASE / E3 ligase / complex / stapled peptide
Function / homology
Function and homology information


positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of mitophagy / ERBB2 signaling pathway / positive regulation of smooth muscle cell apoptotic process / nuclear inclusion body / misfolded protein binding / protein folding chaperone complex ...positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of mitophagy / ERBB2 signaling pathway / positive regulation of smooth muscle cell apoptotic process / nuclear inclusion body / misfolded protein binding / protein folding chaperone complex / cellular response to misfolded protein / ubiquitin-ubiquitin ligase activity / RIPK1-mediated regulated necrosis / ERAD pathway / chaperone-mediated autophagy / protein quality control for misfolded or incompletely synthesized proteins / TPR domain binding / SMAD binding / protein monoubiquitination / negative regulation of smooth muscle cell apoptotic process / protein K63-linked ubiquitination / positive regulation of proteolysis / R-SMAD binding / protein maturation / protein autoubiquitination / endoplasmic reticulum unfolded protein response / ubiquitin ligase complex / Hsp70 protein binding / heat shock protein binding / Downregulation of TGF-beta receptor signaling / positive regulation of protein ubiquitination / response to ischemia / G protein-coupled receptor binding / Regulation of TNFR1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / Hsp90 protein binding / regulation of protein stability / RING-type E3 ubiquitin transferase / tau protein binding / Regulation of necroptotic cell death / Z disc / Downregulation of ERBB2 signaling / kinase binding / Regulation of PTEN stability and activity / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / MAPK cascade / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / cellular response to heat / protein-folding chaperone binding / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / 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
N,N'-(1,4-phenylene)diacetamide / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsLi, K. / Swiecicki, J.-M. / Tokareva, O.S. / Thomson, T.M. / Verdine, G.L. / McGee, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2023
Title: Recognition and reprogramming of E3 ubiquitin ligase surfaces by alpha-helical peptides.
Authors: Tokareva, O.S. / Li, K. / Travaline, T.L. / Thomson, T.M. / Swiecicki, J.M. / Moussa, M. / Ramirez, J.D. / Litchman, S. / Verdine, G.L. / McGee, J.H.
History
DepositionSep 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CHIP
B: H318
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1966
Polymers16,7502
Non-polymers4464
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-30 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.560, 46.960, 53.620
Angle α, β, γ (deg.)90.000, 126.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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: 15350.439 Da / Num. of mol.: 1 / Fragment: TPR domain
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: Protein/peptide H318


Mass: 1399.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 134 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium sulfate, 30% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.47→43.11 Å / Num. obs: 27179 / % possible obs: 96.7 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 18.3
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1284 / CC1/2: 0.758 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NSV

5nsv
PDB Unreleased entry


Resolution: 1.47→26.75 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2119 1362 5.09 %
Rwork0.1921 25415 -
obs0.1931 26777 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.6 Å2 / Biso mean: 26.3905 Å2 / Biso min: 13.26 Å2
Refinement stepCycle: final / Resolution: 1.47→26.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 28 130 1310
Biso mean--36.61 33.9 -
Num. residues----144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.520.3361210.32232490261193
1.52-1.580.2791400.27262473261393
1.58-1.660.23211170.24062506262394
1.66-1.740.26611270.23182552267995
1.74-1.850.27381230.22752527265095
1.85-1.990.25211480.21472538268695
2-2.20.21661460.19632513265995
2.2-2.510.21231390.18712591273096
2.51-3.170.18311400.19242593273396
3.17-26.750.19181610.16082632279397

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