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- PDB-4kbq: Structure of the CHIP-TPR domain in complex with the Hsc70 Lid-Ta... -

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Basic information

Entry
Database: PDB / ID: 4kbq
TitleStructure of the CHIP-TPR domain in complex with the Hsc70 Lid-Tail domains
Components
  • E3 ubiquitin-protein ligase CHIP
  • Heat shock cognate 71 kDa protein
KeywordsLIGASE/PROTEIN BINDING / TPR / E3 ubiquitin ligase / Hsc70 / LIGASE-PROTEIN BINDING complex
Function / homology
Function and homology information


positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / lumenal side of lysosomal membrane / regulation of protein import / protein transmembrane import into intracellular organelle / positive regulation of lysosomal membrane permeability / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / chaperone-mediated autophagy translocation complex disassembly ...positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / lumenal side of lysosomal membrane / regulation of protein import / protein transmembrane import into intracellular organelle / positive regulation of lysosomal membrane permeability / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / lysosomal matrix / A1 adenosine receptor binding / late endosomal microautophagy / protein carrier chaperone / response to nickel cation / Respiratory syncytial virus genome transcription / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Lipophagy / GABA synthesis, release, reuptake and degradation / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / protein targeting to lysosome involved in chaperone-mediated autophagy / response to odorant / C3HC4-type RING finger domain binding / ERBB2 signaling pathway / synaptic vesicle uncoating / positive regulation by host of viral genome replication / positive regulation of mitophagy / positive regulation of smooth muscle cell apoptotic process / clathrin coat disassembly / CHL1 interactions / ATP-dependent protein disaggregase activity / negative regulation of NLRP3 inflammasome complex assembly / regulation of protein complex stability / photoreceptor ribbon synapse / misfolded protein binding / nuclear inclusion body / maintenance of postsynaptic specialization structure / membrane organization / glycinergic synapse / Prp19 complex / presynaptic cytosol / cellular response to misfolded protein / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic specialization membrane / ubiquitin-ubiquitin ligase activity / intermediate filament / RIPK1-mediated regulated necrosis / regulation of postsynapse organization / Lysosome Vesicle Biogenesis / negative regulation of cardiac muscle cell apoptotic process / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / postsynaptic cytosol / Golgi Associated Vesicle Biogenesis / protein quality control for misfolded or incompletely synthesized proteins / TPR domain binding / non-chaperonin molecular chaperone ATPase / phosphatidylserine binding / SMAD binding / protein monoubiquitination / negative regulation of smooth muscle cell apoptotic process / positive regulation of proteolysis / R-SMAD binding / protein K63-linked ubiquitination / protein maturation / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / regulation of protein-containing complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / estrous cycle / protein autoubiquitination / Protein methylation / ATP metabolic process / ubiquitin ligase complex / positive regulation of phagocytosis / endoplasmic reticulum unfolded protein response / ERAD pathway / forebrain development / skeletal muscle tissue development / heat shock protein binding / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to cadmium ion / Hsp70 protein binding / cellular response to starvation / autophagosome / photoreceptor inner segment / lysosomal lumen / mRNA Splicing - Major Pathway / cerebellum development / Downregulation of TGF-beta receptor signaling / kidney development / dendritic shaft / positive regulation of protein ubiquitination
Similarity search - Function
CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Heat shock hsp70 proteins family signature 2. ...CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / ATPase, nucleotide binding domain / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Heat shock cognate 71 kDa protein / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsPage, R.C. / Amick, J. / Nix, J.C. / Misra, S.
CitationJournal: Structure / Year: 2015
Title: A Bipartite Interaction between Hsp70 and CHIP Regulates Ubiquitination of Chaperoned Client Proteins.
Authors: Zhang, H. / Amick, J. / Chakravarti, R. / Santarriaga, S. / Schlanger, S. / McGlone, C. / Dare, M. / Nix, J.C. / Scaglione, K.M. / Stuehr, D.J. / Misra, S. / Page, R.C.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: E3 ubiquitin-protein ligase CHIP
D: Heat shock cognate 71 kDa protein
C: Heat shock cognate 71 kDa protein


Theoretical massNumber of molelcules
Total (without water)54,6164
Polymers54,6164
Non-polymers00
Water93752
1
A: E3 ubiquitin-protein ligase CHIP
C: Heat shock cognate 71 kDa protein


Theoretical massNumber of molelcules
Total (without water)27,3082
Polymers27,3082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-7 kcal/mol
Surface area13090 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase CHIP
D: Heat shock cognate 71 kDa protein


Theoretical massNumber of molelcules
Total (without water)27,3082
Polymers27,3082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-4 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.500, 78.500, 424.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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 / STIP1 homology and U box-containing protein 1


Mass: 15884.057 Da / Num. of mol.: 2 / Fragment: TPR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHIP, PP1131, STUB1 / Plasmid: pHis//2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta
References: UniProt: Q9UNE7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Heat shock cognate 71 kDa protein / Heat shock 70 kDa protein 8


Mass: 11423.743 Da / Num. of mol.: 2 / Fragment: Lid-Tail (delta626-638) / Mutation: delta(626-638) deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSC70, HSP73, HSPA10, HSPA8 / Plasmid: TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P11142
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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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: 3.46 Å3/Da / Density % sol: 64.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.7M ammonium citrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 17, 2012
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.91→64.75 Å / Num. obs: 17188 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.91→3.01 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 4.2 / % possible all: 76.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
SCALAdata scaling
PHENIX(1.8.1_1168)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2C2L, 3LOF

2c2l

3lof


Resolution: 2.91→64.746 Å / SU ML: 0.41 / σ(F): 1.6 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2627 3122 9.98 %
Rwork0.2236 --
obs0.2274 17188 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→64.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 0 52 3559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013563
X-RAY DIFFRACTIONf_angle_d1.2514783
X-RAY DIFFRACTIONf_dihedral_angle_d15.7421378
X-RAY DIFFRACTIONf_chiral_restr0.084505
X-RAY DIFFRACTIONf_plane_restr0.007633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-2.95560.2832600.2963554X-RAY DIFFRACTION43
2.9556-3.0040.35661480.30211323X-RAY DIFFRACTION100
3.004-3.05580.34471470.29871312X-RAY DIFFRACTION100
3.0558-3.11140.36161460.27921311X-RAY DIFFRACTION100
3.1114-3.17130.33561440.26841314X-RAY DIFFRACTION100
3.1713-3.2360.32391450.27691320X-RAY DIFFRACTION100
3.236-3.30630.32931450.25751316X-RAY DIFFRACTION100
3.3063-3.38330.2971400.24341311X-RAY DIFFRACTION100
3.3833-3.46790.2881420.22571304X-RAY DIFFRACTION100
3.4679-3.56160.24061460.21971342X-RAY DIFFRACTION100
3.5616-3.66640.29781410.22361298X-RAY DIFFRACTION100
3.6664-3.78470.26091540.21761314X-RAY DIFFRACTION100
3.7847-3.920.24011520.21381329X-RAY DIFFRACTION100
3.92-4.07690.25151450.20781287X-RAY DIFFRACTION100
4.0769-4.26240.19831450.19641314X-RAY DIFFRACTION100
4.2624-4.48710.22211440.18471302X-RAY DIFFRACTION100
4.4871-4.76820.22281450.18481316X-RAY DIFFRACTION100
4.7682-5.13620.23491450.21091322X-RAY DIFFRACTION100
5.1362-5.65280.26651490.23611327X-RAY DIFFRACTION100
5.6528-6.47010.2981490.25571315X-RAY DIFFRACTION100
6.4701-8.14910.2381470.22641293X-RAY DIFFRACTION100
8.1491-64.76190.26461430.20911328X-RAY DIFFRACTION100

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