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- PDB-8f14: Structure of the STUB1 TPR domain in complex with H201, an all-D ... -

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Basic information

Entry
Database: PDB / ID: 8f14
TitleStructure of the STUB1 TPR domain in complex with H201, an all-D Helicon Polypeptide
Components
  • E3 ubiquitin-protein ligase CHIP
  • all-D Helicon Polypeptide H201
KeywordsLIGASE / E3 ligase / D-peptide / stapled peptide
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 / protein quality control for misfolded or incompletely synthesized proteins / R-SMAD binding / positive regulation of proteolysis / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / protein autoubiquitination / heat shock protein binding / ERAD pathway / Hsp70 protein binding / Downregulation of TGF-beta receptor signaling / response to ischemia / positive regulation of protein ubiquitination / Hsp90 protein binding / Regulation of TNFR1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / G protein-coupled receptor binding / RING-type E3 ubiquitin transferase / regulation of protein stability / Regulation of necroptotic cell death / kinase binding / tau protein binding / Downregulation of ERBB2 signaling / Regulation of PTEN stability and activity / Z disc / protein polyubiquitination / Regulation of RUNX2 expression and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / 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 stabilization / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / enzyme binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol
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 / polypeptide(D) / polypeptide(D) (> 10) / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsLi, K. / Callahan, A.J. / Travaline, T.L. / Tokareva, O.S. / Swiecicki, J.-M. / Verdine, G.L. / Pentelute, B.L. / McGee, J.H.
Funding support Germany, 3items
OrganizationGrant numberCountry
Other privateFOG Pharmaceuticals
Other privateMIT School of Science Fellowship in Cancer Research
German Research Foundation (DFG)LE 4224/1-1 Germany
CitationJournal: Chemrxiv / Year: 2023
Title: Single-Shot Flow Synthesis of D-Proteins for Mirror-Image Phage Display
Authors: Callahan, A.J. / Gandhesiri, S. / Travaline, T.L. / Lozano Salazar, L / Hanna, S. / Lee, Y.-C. / Li, K. / Tokareva, O.S. / Swiecicki, J.-M. / Loas, A. / Verdine, G.L. / McGee, J.H. / Pentelute, B.L.
History
DepositionNov 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: all-D Helicon Polypeptide H201
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7247
Polymers17,2502
Non-polymers4745
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-15 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.158, 90.115, 92.333
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-204-

HOH

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Components

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Protein / Polypeptide(D) , 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
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: Polypeptide(D) all-D Helicon Polypeptide H201


Type: Peptide-like / Class: Substrate analog / Mass: 1899.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002512

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Non-polymers , 4 types, 139 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Sulfate, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.89685 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89685 Å / Relative weight: 1
ReflectionResolution: 1.69→92.33 Å / Num. obs: 21997 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.2
Reflection shellResolution: 1.69→1.72 Å / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1103 / % possible all: 100

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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: 3Q49

3q49


Resolution: 1.69→45.06 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 1106 5.04 %
Rwork0.1965 20839 -
obs0.1984 21945 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.12 Å2 / Biso mean: 34.7675 Å2 / Biso min: 18.47 Å2
Refinement stepCycle: final / Resolution: 1.69→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 32 134 1352
Biso mean--39.38 42.1 -
Num. residues----147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.770.31551460.285725362682100
1.77-1.860.28881410.243125662707100
1.86-1.980.27121330.227325702703100
1.98-2.130.27511320.20925932725100
2.13-2.340.22561290.204826112740100
2.34-2.680.25881500.205825952745100
2.68-3.380.22781340.193726332767100
3.38-45.060.20991410.17672735287699

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