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- PDB-3q49: Crystal structure of the TPR domain of CHIP complexed with Hsp70-... -

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Basic information

Entry
Database: PDB / ID: 3q49
TitleCrystal structure of the TPR domain of CHIP complexed with Hsp70-C peptide
Components
  • Hsp70-C peptide
  • STIP1 homology and U box-containing protein 1
KeywordsLIGASE/CHAPERONE / E3 ubiquitin ligase / LIGASE-CHAPERONE complex
Function / homology
Function and homology information


positive regulation of chaperone-mediated protein complex assembly / Downregulation of TGF-beta receptor signaling / regulation of glucocorticoid metabolic process / Downregulation of ERBB2 signaling / negative regulation of vascular associated smooth muscle contraction / Regulation of TNFR1 signaling / negative regulation of peroxisome proliferator activated receptor signaling pathway / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Regulation of necroptotic cell death ...positive regulation of chaperone-mediated protein complex assembly / Downregulation of TGF-beta receptor signaling / regulation of glucocorticoid metabolic process / Downregulation of ERBB2 signaling / negative regulation of vascular associated smooth muscle contraction / Regulation of TNFR1 signaling / negative regulation of peroxisome proliferator activated receptor signaling pathway / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Regulation of necroptotic cell death / : / denatured protein binding / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of smooth muscle cell apoptotic process / positive regulation of mitophagy / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / negative regulation of cardiac muscle hypertrophy / death receptor agonist activity / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / nuclear inclusion body / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / regulation of mitotic spindle assembly / cellular response to misfolded protein / protein folding chaperone complex / aggresome / lysosomal transport / positive regulation of ubiquitin-protein transferase activity / ubiquitin-ubiquitin ligase activity / cellular response to steroid hormone stimulus / chaperone-mediated autophagy / TPR domain binding / mRNA catabolic process / negative regulation of smooth muscle cell apoptotic process / : / protein quality control for misfolded or incompletely synthesized proteins / R-SMAD binding / positive regulation of proteolysis / regulation of protein ubiquitination / protein K63-linked ubiquitination / Regulation of HSF1-mediated heat shock response / cellular response to unfolded protein / HSF1-dependent transactivation / protein monoubiquitination / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / response to unfolded protein / ubiquitin ligase complex / Mitochondrial unfolded protein response (UPRmt) / Attenuation phase / chaperone-mediated protein complex assembly / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / transcription regulator inhibitor activity / protein autoubiquitination / negative regulation of protein binding / heat shock protein binding / ERAD pathway / inclusion body / negative regulation of protein ubiquitination / protein folding chaperone / Hsp70 protein binding / centriole / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of erythrocyte differentiation / positive regulation of RNA splicing / response to ischemia / positive regulation of protein ubiquitination / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / ATP-dependent protein folding chaperone / Hsp90 protein binding / negative regulation of transforming growth factor beta receptor signaling pathway / : / negative regulation of cell growth / G protein-coupled receptor binding / PKR-mediated signaling / RING-type E3 ubiquitin transferase / kinase binding / histone deacetylase binding / Z disc / protein polyubiquitination / disordered domain specific binding / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / transcription corepressor activity / unfolded protein binding / protein folding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / MAPK cascade / cellular response to heat / virus receptor activity
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 / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. ...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 / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / ATPase, nucleotide binding domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Mainly Alpha
Similarity search - Domain/homology
Heat shock 70 kDa protein 1A / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.543 Å
AuthorsWang, L. / Chen, L. / Wu, J.W.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular Mechanism of the Negative Regulation of Smad1/5 Protein by Carboxyl Terminus of Hsc70-interacting Protein (CHIP).
Authors: Wang, L. / Liu, Y.T. / Hao, R. / Chen, L. / Chang, Z. / Wang, H.R. / Wang, Z.X. / Wu, J.W.
History
DepositionDec 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
B: STIP1 homology and U box-containing protein 1
C: Hsp70-C peptide


Theoretical massNumber of molelcules
Total (without water)16,5932
Polymers16,5932
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-5 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.033, 77.967, 37.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein STIP1 homology and U box-containing protein 1 / Carboxy terminus of Hsp70-interacting protein / E3 ubiquitin-protein ligase CHIP


Mass: 15733.964 Da / Num. of mol.: 1 / Fragment: TPR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stub1, Chip / Plasmid: pET-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9WUD1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Hsp70-C peptide


Mass: 858.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: P0DMV8*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Bis-tris propane pH 7.0, 40% PEG MME 2000, 3% (w/v) xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97924 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.54→33.7 Å / Num. all: 20426 / Num. obs: 20035 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 52.2
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 11.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C2L

2c2l


Resolution: 1.543→33.678 Å / SU ML: 0.15 / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 1027 5.13 %RANDOM
Rwork0.1676 ---
obs0.1695 20035 97.99 %-
all-20426 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.083 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.2402 Å2-0 Å20 Å2
2---3.9653 Å2-0 Å2
3---9.4765 Å2
Refinement stepCycle: LAST / Resolution: 1.543→33.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 0 197 1318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051139
X-RAY DIFFRACTIONf_angle_d0.8651532
X-RAY DIFFRACTIONf_dihedral_angle_d16.574438
X-RAY DIFFRACTIONf_chiral_restr0.058161
X-RAY DIFFRACTIONf_plane_restr0.004205
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5428-1.62420.2351450.1736256395
1.6242-1.72590.20721350.1762263697
1.7259-1.85920.20411350.1749267797
1.8592-2.04620.21831590.1734269699
2.0462-2.34230.19121660.1636272999
2.3423-2.95080.2081530.16952779100
2.9508-33.68580.19551340.1549292899

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