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- PDB-8f15: Structure of the STUB1 TPR domain in complex with H202, an all-D ... -

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Basic information

Entry
Database: PDB / ID: 8f15
TitleStructure of the STUB1 TPR domain in complex with H202, an all-D Helicon Polypeptide
Components
  • E3 ubiquitin-protein ligase CHIP
  • all-D Helicon Polypeptide H202
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 / 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 / chaperone-mediated autophagy / TPR domain binding / protein quality control for misfolded or incompletely synthesized proteins / SMAD binding / protein monoubiquitination / negative regulation of smooth muscle cell apoptotic process / R-SMAD binding / protein K63-linked ubiquitination / positive regulation of proteolysis / protein maturation / protein autoubiquitination / ERAD pathway / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / heat shock protein binding / Hsp70 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 / RING-type E3 ubiquitin transferase / regulation of protein stability / tau protein binding / Regulation of necroptotic cell death / Downregulation of ERBB2 signaling / kinase binding / Z disc / Regulation of PTEN stability and activity / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / MAPK cascade / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / 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: 1.73 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 United States, Germany, 3items
OrganizationGrant numberCountry
Other privateFOG Pharmaceuticals United States
Other privateMIT School of Science Fellowship in Cancer Research United States
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CHIP
B: E3 ubiquitin-protein ligase CHIP
C: E3 ubiquitin-protein ligase CHIP
D: all-D Helicon Polypeptide H202
E: all-D Helicon Polypeptide H202
F: all-D Helicon Polypeptide H202
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,75116
Polymers51,7406
Non-polymers1,01110
Water5,981332
1
A: E3 ubiquitin-protein ligase CHIP
D: all-D Helicon Polypeptide H202
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5635
Polymers17,2472
Non-polymers3163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-4 kcal/mol
Surface area8090 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase CHIP
E: all-D Helicon Polypeptide H202
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6256
Polymers17,2472
Non-polymers3784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-0 kcal/mol
Surface area7900 Å2
MethodPISA
3
C: E3 ubiquitin-protein ligase CHIP
F: all-D Helicon Polypeptide H202
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5635
Polymers17,2472
Non-polymers3163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-7 kcal/mol
Surface area8460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.560, 50.560, 199.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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: 15350.439 Da / Num. of mol.: 3
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 H202


Type: Peptide-like / Class: Substrate analog / Mass: 1896.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002515
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS pH 8, 30% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→49.02 Å / Num. obs: 51998 / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 16.6
Reflection shellResolution: 1.73→1.76 Å / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2848 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q49

3q49


Resolution: 1.73→49.02 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2096 --
Rwork0.18 --
obs-51994 100 %
Refinement stepCycle: LAST / Resolution: 1.73→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3615 0 28 332 3975

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