[English] 日本語
Yorodumi
- PDB-8f17: Structure of the STUB1 TPR domain in complex with H204, an all-D ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 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
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more