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- PDB-9dyb: CHIP-TPR in complex with the phosphorylated Hsp70 tail -

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Basic information

Entry
Database: PDB / ID: 9dyb
TitleCHIP-TPR in complex with the phosphorylated Hsp70 tail
Components
  • E3 ubiquitin-protein ligase CHIP
  • Heat shock 70 kDa protein 1A
KeywordsLIGASE / ubiquitin ligase / chaperone
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 / Regulation of TNFR1 signaling / Hsp90 protein binding / 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 / 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
E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, H. / Nix, J.C. / Page, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128595 United States
Citation
Journal: Biorxiv / Year: 2025
Title: Phosphorylation-State Modulated Binding of HSP70: Structural Insights and Compensatory Protein Engineering.
Authors: Stewart, M. / Paththamperuma, C. / McCann, C. / Cottingim, K. / Zhang, H. / DelVecchio, R. / Peng, I. / Fennimore, E. / Nix, J.C. / Saeed, M.N. / George, K. / Makaroff, K. / Colie, M. / ...Authors: Stewart, M. / Paththamperuma, C. / McCann, C. / Cottingim, K. / Zhang, H. / DelVecchio, R. / Peng, I. / Fennimore, E. / Nix, J.C. / Saeed, M.N. / George, K. / Makaroff, K. / Colie, M. / Paulakonis, E. / Almeida, M.F. / Afolayan, A.J. / Brown, N.G. / Page, R.C. / Schisler, J.C.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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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: Heat shock 70 kDa protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8583
Polymers16,8232
Non-polymers351
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-12 kcal/mol
Surface area7730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.575, 45.932, 78.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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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: 15884.057 Da / Num. of mol.: 1 / Fragment: TPR domain
Source method: isolated from a genetically manipulated source
Details: residues "GAMGS" at N-terminus added during cloning as part of the fusion protein
Source: (gene. exp.) Homo sapiens (human) / Gene: STUB1, CHIP, PP1131 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UNE7, RING-type E3 ubiquitin transferase
#2: Protein/peptide Heat shock 70 kDa protein 1A


Mass: 938.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: phosphorylated threonine / Source: (synth.) Homo sapiens (human) / References: EC: 3.6.1.3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5, 30% (w/v) PEG 4000, 10 mM zinc chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→39.6 Å / Num. obs: 34506 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.58 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.09171 / Rpim(I) all: 0.05546 / Net I/σ(I): 10.32
Reflection shellResolution: 1.59→1.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.8595 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 8914 / CC1/2: 0.612 / CC star: 0.871 / Rpim(I) all: 0.5321 / % possible all: 97.38

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.6 Å / SU ML: 0.1402 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.8729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2203 1855 10.01 %
Rwork0.1797 16676 -
obs0.1837 18531 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 0 1 144 1255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571144
X-RAY DIFFRACTIONf_angle_d0.78221544
X-RAY DIFFRACTIONf_chiral_restr0.0431162
X-RAY DIFFRACTIONf_plane_restr0.0069207
X-RAY DIFFRACTIONf_dihedral_angle_d14.005439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.2691380.23171237X-RAY DIFFRACTION97.38
1.64-1.690.27871380.23691244X-RAY DIFFRACTION99.86
1.69-1.740.28511390.22351260X-RAY DIFFRACTION99.86
1.74-1.810.25021420.20611277X-RAY DIFFRACTION99.65
1.81-1.880.24451400.19771251X-RAY DIFFRACTION99.78
1.88-1.960.25751420.1881274X-RAY DIFFRACTION99.79
1.96-2.070.21761420.18511273X-RAY DIFFRACTION100
2.07-2.20.22511410.1681271X-RAY DIFFRACTION100
2.2-2.370.20711430.16581287X-RAY DIFFRACTION100
2.37-2.60.21621420.18041279X-RAY DIFFRACTION100
2.6-2.980.23741460.18241300X-RAY DIFFRACTION100
2.98-3.750.20491470.16451328X-RAY DIFFRACTION100
3.76-39.60.18041550.16241395X-RAY DIFFRACTION99.81
Refinement TLS params.Method: refined / Origin x: -16.4368358194 Å / Origin y: -16.9316581791 Å / Origin z: 9.65319995079 Å
111213212223313233
T0.081270484926 Å2-0.00877817994586 Å20.00789872026958 Å2-0.0972587900148 Å2-0.00820006410689 Å2--0.0804907415834 Å2
L0.372290563461 °2-0.239107413507 °20.36045631004 °2-1.1474622754 °2-0.780584331721 °2--1.12619690227 °2
S9.85614371198E-5 Å °0.0285811436183 Å °0.0158953063391 Å °-0.0332015542508 Å °-0.00821281009265 Å °-0.0134495454851 Å °-0.0435398873839 Å °0.0238702070311 Å °0.0116876481813 Å °
Refinement TLS groupSelection details: all

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