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- PDB-8ehz: Crystal structure of the STUB1 TPR domain in complex with H317, a... -

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Basic information

Entry
Database: PDB / ID: 8ehz
TitleCrystal structure of the STUB1 TPR domain in complex with H317, a Helicon Polypeptide
Components
  • E3 ubiquitin-protein ligase CHIP
  • H317
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 / 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 / tau protein binding / kinase 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 / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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
Revision 1.2Nov 20, 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

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Assembly

Deposited unit
C: H317
D: H317
A: E3 ubiquitin-protein ligase CHIP
B: E3 ubiquitin-protein ligase CHIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7086
Polymers34,3234
Non-polymers3842
Water32418
1
C: H317
A: E3 ubiquitin-protein ligase CHIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3543
Polymers17,1622
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-9 kcal/mol
Surface area7800 Å2
MethodPISA
2
D: H317
B: E3 ubiquitin-protein ligase CHIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3543
Polymers17,1622
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-10 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.209, 63.209, 69.816
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein/peptide H317


Mass: 1277.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: 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: 15884.057 Da / Num. of mol.: 2 / 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
#3: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Sodium acetate, 0.1M sodium citrate pH6.0, 10% PEG4000

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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: 2.06→43.08 Å / Num. obs: 19293 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 44.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.2
Reflection shellResolution: 2.06→2.12 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1471 / CC1/2: 0.938 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NSV

6nsv


Resolution: 2.06→43.08 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 39.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 1935 10.06 %
Rwork0.2409 17301 -
obs0.2439 19236 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.22 Å2 / Biso mean: 60.7906 Å2 / Biso min: 29.48 Å2
Refinement stepCycle: final / Resolution: 2.06→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 28 18 2279
Biso mean--71.12 49.92 -
Num. residues----278
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.06-2.110.33781370.34521232136999
2.11-2.170.37911310.32931224135599
2.17-2.230.30411390.304512351374100
2.23-2.30.35091460.301912211367100
2.31-2.390.32991340.312712291363100
2.39-2.480.3321460.289412651411100
2.48-2.60.31191310.271312381369100
2.6-2.730.34171380.324112321370100
2.73-2.90.31431280.304612261354100
2.9-3.130.28941390.296512681407100
3.13-3.440.30991430.26212091352100
3.44-3.940.27721400.231212701410100
3.94-4.960.2361470.196712201367100
4.96-43.080.19351360.169512321368100

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