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- PDB-8f17: Structure of the STUB1 TPR domain in complex with H204, an all-D ... -

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Basic information

Entry
Database: PDB / ID: 8f17
TitleStructure of the STUB1 TPR domain in complex with H204, an all-D Helicon Polypeptide
Components
  • E3 ubiquitin-protein ligase CHIP
  • all-D Helicon Polypeptide H204
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 / cellular response to misfolded protein ...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 / cellular response to misfolded protein / protein folding chaperone complex / ubiquitin-ubiquitin ligase activity / RIPK1-mediated regulated necrosis / chaperone-mediated autophagy / protein quality control for misfolded or incompletely synthesized proteins / TPR domain binding / protein monoubiquitination / SMAD binding / 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 / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / protein-folding chaperone binding / cellular response to heat / 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 / 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: 2.21 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 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / citation_author / entity / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conf / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _citation_author.name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_work / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _reflns.percent_possible_obs / _reflns_shell.number_unique_obs / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 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: all-D Helicon Polypeptide H204
D: all-D Helicon Polypeptide H204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6387
Polymers34,1914
Non-polymers4463
Water93752
1
A: E3 ubiquitin-protein ligase CHIP
C: all-D Helicon Polypeptide H204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2883
Polymers17,0962
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-10 kcal/mol
Surface area7730 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase CHIP
D: all-D Helicon Polypeptide H204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3504
Polymers17,0962
Non-polymers2542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-13 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.030, 72.710, 59.790
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2
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 H204


Mass: 1745.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Sodium chloride, 0.1 M TRIS pH 8, 8% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18057 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18057 Å / Relative weight: 1
ReflectionResolution: 2.21→46.01 Å / Num. obs: 16124 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 16.9
Reflection shellResolution: 2.21→2.28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 98.6

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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: 2.21→46.01 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 764 5.03 %
Rwork0.216 --
obs0.218 15190 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.18 Å2
Refinement stepCycle: LAST / Resolution: 2.21→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 32 52 2404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.380.33531380.28832864X-RAY DIFFRACTION93
2.38-2.620.33041600.26382825X-RAY DIFFRACTION93
2.62-30.29141450.25842898X-RAY DIFFRACTION93
3-3.780.29541660.22542883X-RAY DIFFRACTION94
3.78-46.010.19831550.17952956X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 8.0407 Å / Origin y: 0.8035 Å / Origin z: 15.5363 Å
111213212223313233
T0.1691 Å20.0258 Å20.0409 Å2-0.2132 Å2-0.0053 Å2--0.2035 Å2
L0.4536 °20.0161 °20.79 °2-0.5684 °2-0.0534 °2--1.2151 °2
S-0.0064 Å °-0.0468 Å °0.0109 Å °-0.1097 Å °-0.0028 Å °0.0192 Å °0.0201 Å °0.0415 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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